diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..e5aa5b3 --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +.idea +*.iml +target \ No newline at end of file diff --git a/pom.xml b/pom.xml index 5d5ea82..f129f1f 100644 --- a/pom.xml +++ b/pom.xml @@ -105,26 +105,7 @@ - - - org.jacoco - jacoco-maven-plugin - 0.5.7.201204190339 - - - - prepare-agent - - - - report - prepare-package - - report - - - - + diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/AminoAcidInterface.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/AminoAcidInterface.java index 451ac82..9764629 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/AminoAcidInterface.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/AminoAcidInterface.java @@ -15,7 +15,7 @@ public interface AminoAcidInterface { /** * fetches the amino acids from the proteome discoverer database - * @param iConnection connection to a msf file + * @param msfFile the proteome discoverer file to retrieve the amino acids for * @return a List containing all the amino acids stored in the msf file * @throws java.sql.SQLException if something went wrong with the retrieving */ diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/CustomDataInterface.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/CustomDataInterface.java index 1d16740..2e40b22 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/CustomDataInterface.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/CustomDataInterface.java @@ -15,7 +15,7 @@ public interface CustomDataInterface { /** * - * @param iConnection a connection to the msf file + * @param msfFile the proteome discoverer file to retrieve the custom data from * @return a hashmap containing the custom fields key: fieldid in the db * value: displayname given in the db */ @@ -27,9 +27,8 @@ public interface CustomDataInterface { /** * - * @param msfFileConnection connection to the msf file + * @param msfFile the proteome discoverer file to retrieve the custom spectrum data from * @return an List with the custom spectra data - * @throws SQLException */ public List getCustomSpectraData(Map iCustomDataFieldsMap, MsfFile msfFile); diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ModificationInterface.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ModificationInterface.java index 8a39ab9..a4af9cb 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ModificationInterface.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ModificationInterface.java @@ -37,7 +37,7 @@ public interface ModificationInterface { /** creates a hashmap containing the modifications stored in the msf file - @param iConnection: a connection to the SQLite database + @param msfFile the proteome discoverer file to retrieve the modifications from @return hashmap containing the modifications @throws SQLException if something went wrong with the retrieving */ @@ -46,8 +46,8 @@ public interface ModificationInterface { /** * fetch all the abbreviated names of the modifications used in the msf file - * - * @param aConnection a connection to the SQLite database + * + @param msfFile the proteome discoverer file to retrieve the modification names from * @return a List containing all the names of the modifications used in the msf file */ diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/PeptideInterface.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/PeptideInterface.java index 889e1f6..6ca6f4d 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/PeptideInterface.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/PeptideInterface.java @@ -16,8 +16,7 @@ public interface PeptideInterface { /** @param protein: a Protein object - @param iMsfVersion: enumeration object containing the version number of the current Msf file - @param iAminoAcids a List containing the objects returned from the AminoAcid + @param msfFile the proteome discoverer file to retrieve from @return a List containing all the peptides connected to the given Protein, empty if none are found */ @@ -25,9 +24,7 @@ public interface PeptideInterface { /** @param lProteinAccession: a string containing the accession of the protein - @param msfFileConnection: a connection to the SQLite database - @param iMsfVersion: enumeration object containing the version number of the current Msf file - @param iAminoAcids a List containing the objects returned from the AminoAcid + @param msfFile the proteome discoverer file to retrieve from @return a List containing all the peptides connected to the given protein accession, empty if none are found */ @@ -46,9 +43,7 @@ public interface PeptideInterface { /** * * @param confidenceLevel the confidence level of the peptides wanted - * @param msfFileConnection connection to the msf file - * @param iMsfVersion the version with which the msf file is made - * @param iAminoAcids vector with the amino acids fetched from the amino acid lowmem class + @param msfFile the proteome discoverer file to retrieve from * @return a vector containing the peptides identified and the specified confidence level, empty if none are found */ public List getPeptidesWithConfidenceLevel(int confidenceLevel,MsfFile msfFile); @@ -56,23 +51,21 @@ public interface PeptideInterface { /** * @param confidenceLevel the confidence level of the peptides wanted - * @param aConnection connection to the msf file + @param msfFile the proteome discoverer file to retrieve from */ public int getNumberOfPeptidesForConfidenceLevel(int confidenceLevel,MsfFile msfFile); /** * @param proteinLowMemList a vector containing the protein objects we want to retrieve the peptides for - * @param msfFileConnection a connection to the msf file - * @param iAminoAcids a vector of the amino acids retrieved from the msf file - * @param iMsfVersion the msf file version + @param msfFile the proteome discoverer file to retrieve from * @param confidenceLevel the confidence level we want to retrieve the peptides at */ public void getPeptidesForProteinList(List proteinLowMemList,MsfFile msfFile,int confidenceLevel); /** - * - * @param msfFileConnection connection to the msf file + * + @param msfFile the proteome discoverer file to retrieve from */ public int returnNumberOfPeptides(MsfFile msfFile); diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ProteinControllerInterface.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ProteinControllerInterface.java index abaf57f..1c2018d 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ProteinControllerInterface.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ProteinControllerInterface.java @@ -18,21 +18,16 @@ public interface ProteinControllerInterface { /** a method to fetch all the proteins stored in the msf file - @param iConnection connection to the msf file + @param msfFile the proteome discoverer file to retrieve from @return an iterator containing all the proteins in Protein objects - @throws SQLException if something went wrong with the retrieving */ public List getAllProteins(MsfFile msfFile); /** get a protein from an accession - - @return a Protein object - @throws SQLException if something went wrong with the retrieving - * @param proteinAccession an accession - * @param iConnection a connection to the msf file + @param msfFile the proteome discoverer file to retrieve from */ public ProteinLowMem getProteinFromAccession(String proteinAccession, MsfFile msfFile); @@ -41,9 +36,8 @@ public interface ProteinControllerInterface { get the accession from a protein @param proteinID a protein id in the db - @param iConnection a connection to the msf file + @param msfFile the proteome discoverer file to retrieve from @return the accession for a given Protein object - @throws SQLException if something went wrong with the retrieving */ public String getAccessionFromProteinID(int proteinID,MsfFile msfFile); @@ -52,9 +46,8 @@ public interface ProteinControllerInterface { * get the sequence stored in the db for a given ProteinID * * @param proteinID the ID of the protein in the SQLite DB - * @param iConnection connection to the SQLite DB + @param msfFile the proteome discoverer file to retrieve from * @return string containing the sequence stored in the DB - * @throws SQLException if something went wrong with the retrieving */ public String getSequenceForProteinID(int proteinID,MsfFile msfFile); @@ -63,9 +56,8 @@ public interface ProteinControllerInterface { * method for retrieving all the proteins connected to a given peptide in the DB * * @param PeptideID peptideID stored in the SQLite DB - * @param iConnection connection to the SQLite DB + @param msfFile the proteome discoverer file to retrieve from * @return a vector containing all Protein objects connected to a given peptide - * @throws SQLException if something went wrong with the retrieving */ public List getProteinsForPeptide(int PeptideID,MsfFile msfFile); } diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/RatioTypeInterface.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/RatioTypeInterface.java index 2dc1f86..1319ed0 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/RatioTypeInterface.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/RatioTypeInterface.java @@ -16,9 +16,8 @@ public interface RatioTypeInterface { /** * - * @param aConnection connection to the SQLite db + @param msfFile the proteome discoverer file to retrieve from * @return vector containing the ratio types - * @throws java.sql.SQLException if something went wrong with the retrieving */ public List parseRatioTypes(MsfFile msfFile); diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/RawFileInterface.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/RawFileInterface.java index 0a950d3..8e8d80d 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/RawFileInterface.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/RawFileInterface.java @@ -14,14 +14,14 @@ public interface RawFileInterface { /** * * @param fileID the file id stored in the msf file - * @param aConnection connection to the msf file + @param msfFile the proteome discoverer file to retrieve from * @return hashmap connecting the file name entry to the fileID */ public Map getRawFileForFileID(int fileID, MsfFile msfFile); /** * - * @param aConnection connection to the msf file + @param msfFile the proteome discoverer file to retrieve from * @return a vector containing all the names of the stored raw files */ public List getRawFileNames(MsfFile msfFile); @@ -29,8 +29,8 @@ public interface RawFileInterface { /** * * @param fileID the file id stored in the msf file - * @param aConnection connection to the msf file + @param msfFile the proteome discoverer file to retrieve from * @return a processed filename (eg sample4_1.raw) */ - public String getRawFileNameForFileID(int FileID, MsfFile msfFile); + public String getRawFileNameForFileID(int fileID, MsfFile msfFile); } diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ScoreTypeInterface.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ScoreTypeInterface.java index 51fcd80..7e7ee41 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ScoreTypeInterface.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/ScoreTypeInterface.java @@ -21,7 +21,7 @@ public interface ScoreTypeInterface { /** method to fetch the score types stored in the msf file - @param aConnection a connection to the msf file + @param msfFile the proteome discoverer file to retrieve from @return a Hashmap containing the score types * @throws java.sql.SQLException if something went wrong with the retrieving */ @@ -30,7 +30,7 @@ public interface ScoreTypeInterface { /** * @param peptideLowMemList a vector containing the peptides we want to retrieve the scores for - * @param aConnection a connection to the msf file + @param msfFile the proteome discoverer file to retrieve from */ public void getScoresForPeptideList(ListpeptideLowMemList,MsfFile msfFile); @@ -38,7 +38,7 @@ public interface ScoreTypeInterface { /** * * @param peptide a peptide to which we want to add the scores - * @param aConnection a connection to the msf file + @param msfFile the proteome discoverer file to retrieve from */ public void addScoresToPeptide (PeptideLowMem peptide, MsfFile msfFile); @@ -46,7 +46,7 @@ public interface ScoreTypeInterface { /** * * @param peptide a peptide to return the different score types for - * @param aConnection a connection to the msf file + @param msfFile the proteome discoverer file to retrieve from * @return a hashMap with key scoreID value: scoreValue * @throws SQLException */ diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/AminoAcidLowMemController.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/AminoAcidLowMemController.java index 45e9678..8b62803 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/AminoAcidLowMemController.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/AminoAcidLowMemController.java @@ -17,7 +17,7 @@ public class AminoAcidLowMemController implements AminoAcidInterface { /** * - * @param aConnection a connection to the msf file + * @param msfFile the proteome discoverer file to retrieve the amino acids from * @return a vector containing all the amino acids in the database * @throws SQLException */ diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ChromatogramLowMemController.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ChromatogramLowMemController.java index 6619562..c2fccf9 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ChromatogramLowMemController.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ChromatogramLowMemController.java @@ -24,7 +24,7 @@ public class ChromatogramLowMemController { * returns the chromatogram for a given peptide ID in the SQLite db * * @param peptideID the id of the peptide - * @param iConnection connection to the msf SQLite file + * @param msfFile the proteome discoverer file to retrieve the chromatograms from * @return a vector containing the chromatogram files */ //TODO check of this returns one or multiple files diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/CustomDataLowMemController.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/CustomDataLowMemController.java index b18e4f8..eaca1ba 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/CustomDataLowMemController.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/CustomDataLowMemController.java @@ -80,8 +80,8 @@ public List getCustomPeptideData(Map /** * adds the custom data of a protein to that protein object * - * @param protein the protein (low memory instance) object - * @param iConnection connection to the msf file + * @param protein the {@link ProteinLowMem} to add the custom data to + * @param msfFile msf File to get the protein data from * @throws SQLException */ @Override diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ModificationLowMemController.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ModificationLowMemController.java index 76ffae5..6444b2d 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ModificationLowMemController.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ModificationLowMemController.java @@ -177,35 +177,15 @@ public List getAllModifications(MsfFile msfFile) { return getModList(msfFile, true, true); } - /** - * - * @param msfFileConnection - * @param msfVersion - * @param returnFixed - * @return - */ + public List getListOfFixedModificationNumbers(MsfFile msfFile) { return getModList(msfFile, true, false); } - /** - * - * @param msfFileConnection - * @param msfVersion - * @return - */ public List getListOfVariableModidifcationNumbers(MsfFile msfFile) { return getModList(msfFile, false, true); } - /** - * - * @param msfFileConnection - * @param msfVersion - * @param getFixedModifications - * @param getVariableModifications - * @return - */ private List getModList(MsfFile msfFile, boolean getFixedModifications, boolean getVariableModifications) { StringBuilder modNumbersToFetch = new StringBuilder("("); List modsToReturn = new ArrayList(); @@ -274,12 +254,7 @@ private List getModList(MsfFile msfFile, boolean getFixedModificat return modsToReturn; } - /** - * - * @param modification - * @param aminoAcids - * @param msfFile - */ + private void addAminoAcidsToModification(Modification modification, List aminoAcids, MsfFile msfFile) { try { PreparedStatement stat = null; diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/PeptideLowMemController.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/PeptideLowMemController.java index c42fc62..c1eeb6c 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/PeptideLowMemController.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/PeptideLowMemController.java @@ -14,7 +14,6 @@ import java.util.HashMap; import java.util.Observable; import java.util.List; -import sun.reflect.generics.reflectiveObjects.NotImplementedException; /** * Created by IntelliJ IDEA. User: Davy Date: 10/1/12 Time: 10:30 AM To change @@ -37,12 +36,8 @@ public List getPeptidesForProteinAtConfidenceLevel(ProteinLowMem /** * * @param protein: a Protein object - * @param iMsfVersion: enumeration object containing the version number of - * the current Msf file - * @param iAminoAcids a List containing the objects returned from the - * AminoAcid + * @param msfFile the proteome discoverer file to retrieve from * @return a vector containing all the peptides connected to the protein - * @throws java.sql.SQLException */ @Override public List getPeptidesForProtein(ProteinLowMem protein, MsfFile msfFile) { @@ -146,7 +141,7 @@ public List getInformationForPeptide(int peptideID, MsfFile msfFile, boolean ful ResultSet rs = null; try { if (fullInfo) { - rs = stat.executeQuery("select Peptides.Sequence, SpectrumHeaders.FirstScan,SpectrumHeaders.LastScan,Peptides.Annotations,ProcessingNodes.FriendlyName from Peptides where ConfidenceLevel >= "); + rs = stat.executeQuery("select Peptides.Sequence, SpectrumHeaders.FirstScan,SpectrumHeaders.LastScan,Peptides.Annotations,ProcessingNodes.FriendlyName from Peptides where ConfidenceLevel >= 1 "); } else { rs = stat.executeQuery(""); } @@ -352,15 +347,9 @@ public int returnNumberOfPeptides(MsfFile msfFile) { } return numberOfPeptides; } -/** - * - * @param protein - * @param msfFile - * @param processingNode - * @return - */ + public List getPeptidesForProteinAndProcessingNode(ProteinLowMem protein, MsfFile msfFile, ProcessingNode processingNode) { processingNode.getProcessingNodeId(); - throw new NotImplementedException(); + throw new UnsupportedOperationException("not yet implemented"); } } \ No newline at end of file diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ProteinGroupLowMemController.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ProteinGroupLowMemController.java index 6813a9d..9db2e05 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ProteinGroupLowMemController.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ProteinGroupLowMemController.java @@ -16,12 +16,7 @@ public class ProteinGroupLowMemController { private static final Logger logger = Logger.getLogger(ProteinGroupLowMemController.class); - /** - * - * @param proteinID - * @param msfFile - * @return - */ + public int getProteinGroupIDForProteinID(int proteinID, MsfFile msfFile) { int proteinGroupID = 0; try { @@ -47,12 +42,7 @@ public int getProteinGroupIDForProteinID(int proteinID, MsfFile msfFile) { return proteinGroupID; } - /** - * - * @param proteinID - * @param msfFile - * @return - */ + public ProteinGroupLowMem getProteinGroupForProteinID(int proteinID, MsfFile msfFile) { return new ProteinGroupLowMem(getProteinGroupIDForProteinID(proteinID, msfFile)); diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/QuanResultLowMemController.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/QuanResultLowMemController.java index 981e73c..79e6d61 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/QuanResultLowMemController.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/QuanResultLowMemController.java @@ -21,7 +21,7 @@ public class QuanResultLowMemController { /** * - * @param aConnection a connection to the msf file + * @param msfFile * @param msfFile the proteome discoverer file to retrieve the isotope patterns from * @return a hashmap with key: the isotope pattern id and value: the * isotopePattern */ diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/RatioTypeLowMemController.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/RatioTypeLowMemController.java index 9fd3a8e..0b4b798 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/RatioTypeLowMemController.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/RatioTypeLowMemController.java @@ -19,8 +19,8 @@ public class RatioTypeLowMemController implements RatioTypeInterface { private static final Logger logger = Logger.getLogger(RatioTypeLowMemController.class); - private List iComponents; - private List iQuanChannelIds; + private List iComponents = new ArrayList(); + private List iQuanChannelIds = new ArrayList(); private final Map quanChannelID = new HashMap(); @Override diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/SpectrumLowMemController.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/SpectrumLowMemController.java index f7373e2..94f091f 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/SpectrumLowMemController.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/SpectrumLowMemController.java @@ -310,7 +310,7 @@ public SpectrumLowMem getSpectrumForSpectrumID(int spectrumOfInterestID, MsfFile @Override public String getSpectrumTitle(String rawFileName, SpectrumLowMem lspectrum) { String spectrumTitle = rawFileName.substring(0, rawFileName.toLowerCase().lastIndexOf(".")); - return new StringBuilder().append(spectrumTitle).append("_").append(lspectrum.getSpectrumId()).append("_").append(lspectrum.getFirstScan()).append("_").append(lspectrum.getCharge()).toString(); + return spectrumTitle + "_" + lspectrum.getSpectrumId() + "_" + lspectrum.getFirstScan() + "_" + lspectrum.getCharge(); } //TODO redo this part properly diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/ProteinLowMem.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/ProteinLowMem.java index ef24427..6a960b9 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/ProteinLowMem.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/ProteinLowMem.java @@ -27,7 +27,6 @@ public class ProteinLowMem implements ProteinModel { * constructor for the ProteinLowMem object * * @param aAccession the protein accession - * @param aConnection a connection to the SQLite database * @param aProteinID the protein id in the SQLite database */ diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/ScoreTypeLowMem.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/ScoreTypeLowMem.java index 78a2e1f..954f69d 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/ScoreTypeLowMem.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/ScoreTypeLowMem.java @@ -39,17 +39,6 @@ public ScoreTypeLowMem(int aScoreID, String aScoreName, String aFriendlyName, St this.iIsMainScore = isMainScore; } - /** - * - * @param iConnection a connection to the msf file - * @return a vector containing all the scoretypes stored in the msf file - * @throws SQLException - */ - /** - * - * @return a vector containing all the scoretypes stored in the msf file - * @throws SQLException - */ public int getScoreTypeId() { return iScoreTypeId; } diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/SpectrumLowMem.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/SpectrumLowMem.java index ead2cbe..53fbfb2 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/SpectrumLowMem.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/model/SpectrumLowMem.java @@ -258,16 +258,16 @@ public void setQuanResult(QuanResultLowMem lQuanResult) { //TODO this looks wrong public boolean isHighestScoring(PeptideLowMem iSelectedPeptide, List scoreTypes) { Boolean lIsHighestScore = null; - for (int l = 0; l < scoreTypes.size(); l++) { - if (iSelectedPeptide.getScoreByScoreType(scoreTypes.get(l)) != null) { - Double lScore = iSelectedPeptide.getScoreByScoreType(scoreTypes.get(l)); + for (ScoreTypeLowMem scoreType : scoreTypes) { + if (iSelectedPeptide.getScoreByScoreType(scoreType) != null) { + Double lScore = iSelectedPeptide.getScoreByScoreType(scoreType); if (lIsHighestScore == null) { lIsHighestScore = true; } if (lScore != null) { - for (int i = 0; i < iPeptides.size(); i++) { - if (!iSelectedPeptide.getModifiedPeptideSequence().equalsIgnoreCase(iPeptides.get(i).getModifiedPeptideSequence())) { - Double lCompareScore = iPeptides.get(i).getScoreByScoreType(scoreTypes.get(l)); + for (PeptideLowMem iPeptide : iPeptides) { + if (!iSelectedPeptide.getModifiedPeptideSequence().equalsIgnoreCase(iPeptide.getModifiedPeptideSequence())) { + Double lCompareScore = iPeptide.getScoreByScoreType(scoreType); if (lCompareScore != null) { if (lScore < lCompareScore) { lIsHighestScore = false; @@ -287,9 +287,9 @@ public boolean isHighestScoring(PeptideLowMem iSelectedPeptide, List scoreTypes) { Boolean lIsLowestScore = null; - for (int i = 0; i < scoreTypes.size(); i++) { - if (iSelectedPeptide.getScoreByScoreType(scoreTypes.get(i)) != null) { - Double lScore = iSelectedPeptide.getScoreByScoreType(scoreTypes.get(i)); + for (ScoreTypeLowMem scoreType : scoreTypes) { + if (iSelectedPeptide.getScoreByScoreType(scoreType) != null) { + Double lScore = iSelectedPeptide.getScoreByScoreType(scoreType); if (lIsLowestScore == null) { lIsLowestScore = true; } diff --git a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/proteinsorter/ProteinSorterByAccession.java b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/proteinsorter/ProteinSorterByAccession.java index be38a11..14e4b19 100644 --- a/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/proteinsorter/ProteinSorterByAccession.java +++ b/thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/proteinsorter/ProteinSorterByAccession.java @@ -21,6 +21,7 @@ public class ProteinSorterByAccession implements Comparator, Seria public ProteinSorterByAccession(boolean lAtoZ){ this.iAtoZ = lAtoZ; } + @Override public int compare(ProteinModel o1, ProteinModel o2) { int comparator; diff --git a/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/ModificationLowMemControllerTest.java b/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/ModificationLowMemControllerTest.java index 45081df..4c2bda4 100644 --- a/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/ModificationLowMemControllerTest.java +++ b/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/ModificationLowMemControllerTest.java @@ -20,9 +20,6 @@ public class ModificationLowMemControllerTest { private static MsfFile msfFile; - public ModificationLowMemControllerTest() { - } - @BeforeClass public static void setUpClass() throws ClassNotFoundException, SQLException { msfFile = new MsfFile(new File(ModificationLowMemControllerTest.class.getClassLoader().getResource("test-msf-v-1.2.msf").getPath())); diff --git a/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/ProteinLowMemControllerTest.java b/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/ProteinLowMemControllerTest.java index 572e198..c5f7250 100644 --- a/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/ProteinLowMemControllerTest.java +++ b/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/ProteinLowMemControllerTest.java @@ -23,10 +23,6 @@ public class ProteinLowMemControllerTest { static MsfFile msfFile; - public ProteinLowMemControllerTest(MsfFile msfFile) { - this.msfFile = msfFile; - } - @BeforeClass public static void setUpClass() throws ClassNotFoundException, SQLException { msfFile = new MsfFile(new File(ProteinLowMemControllerTest.class.getClassLoader().getResource("test-msf-v-1.2.msf").getPath())); diff --git a/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/SpectrumLowMemControllerTest.java b/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/SpectrumLowMemControllerTest.java index 1355bef..e2ba60d 100644 --- a/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/SpectrumLowMemControllerTest.java +++ b/thermo_msf_parser_API/src/test/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/version_1_2/SpectrumLowMemControllerTest.java @@ -76,7 +76,8 @@ public void testCreateSpectrumXMLForSpectrum() throws Exception { System.out.println("createSpectrumXMLForSpectrum"); SpectrumLowMemController instance = new SpectrumLowMemController(); instance.createSpectrumXMLForSpectrum(lSpectrum, msfFile); - FileUtils.writeStringToFile(new File("C:\\Users\\Davy\\spectrumoutput"), lSpectrum.getSpectrumXML()); + FileUtils.writeStringToFile(new File("/spectrumoutput"), lSpectrum.getSpectrumXML()); + //TODO test this file } /**