fixed javadoc

.gitignore

@@ -0,0 +1,3 @@
+.idea
+*.iml
+target

pom.xml

@@ -105,26 +105,7 @@
                         </execution>
                     </executions>
                 </plugin>
-
-                <plugin>
-                    <groupId>org.jacoco</groupId>
-                    <artifactId>jacoco-maven-plugin</artifactId>
-                    <version>0.5.7.201204190339</version>
-                    <executions>
-                        <execution>
-                            <goals>
-                                <goal>prepare-agent</goal>
-                            </goals>
-                        </execution>
-                        <execution>
-                            <id>report</id>
-                            <phase>prepare-package</phase>
-                            <goals>
-                                <goal>report</goal>
-                            </goals>
-                        </execution>
-                    </executions>
-                </plugin>
+
             </plugins>
         </pluginManagement>
     </build>

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
     */

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<CustomDataField> getCustomSpectraData(Map<Integer, CustomDataField> iCustomDataFieldsMap, MsfFile msfFile);

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
      */ 
 

thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/PeptideInterface.java

@@ -16,18 +16,15 @@ 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
     */
 
     public List getPeptidesForProtein(ProteinLowMem protein,MsfFile msfFile);
 
    /**
    @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
    */
 
@@ -46,33 +43,29 @@ 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<PeptideLowMem> getPeptidesWithConfidenceLevel(int confidenceLevel,MsfFile msfFile);
 
 
     /**
      * @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<ProteinLowMem> 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);

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<ProteinLowMem> getProteinsForPeptide(int PeptideID,MsfFile msfFile);
 }

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<RatioTypeLowMem> parseRatioTypes(MsfFile msfFile);

thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/interfaces/RawFileInterface.java

@@ -14,23 +14,23 @@ 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<Integer, String> 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<RawFileLowMem> getRawFileNames(MsfFile msfFile);
 
     /**
      *
      * @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);
 }

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
     */
@@ -30,23 +30,23 @@ 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(List<PeptideLowMem>peptideLowMemList,MsfFile msfFile);
 
     /**
      * 
      * @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);
 
      /**
      *
      * @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
      */

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
      */

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

thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/CustomDataLowMemController.java

@@ -80,8 +80,8 @@ public List<CustomDataField> getCustomPeptideData(Map<Integer, CustomDataField>
     /**
      * 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

thermo_msf_parser_API/src/main/java/com/compomics/thermo_msf_parser_API/lowmeminstance/controllers/ModificationLowMemController.java

@@ -177,35 +177,15 @@ public List<Modification> getAllModifications(MsfFile msfFile) {
         return getModList(msfFile, true, true);
     }
 
-    /**
-     *
-     * @param msfFileConnection
-     * @param msfVersion
-     * @param returnFixed
-     * @return
-     */
+
     public List<Modification> getListOfFixedModificationNumbers(MsfFile msfFile) {
         return getModList(msfFile, true, false);
     }
 
-    /**
-     *
-     * @param msfFileConnection
-     * @param msfVersion
-     * @return
-     */
     public List<Modification> getListOfVariableModidifcationNumbers(MsfFile msfFile) {
         return getModList(msfFile, false, true);
     }
 
-    /**
-     *
-     * @param msfFileConnection
-     * @param msfVersion
-     * @param getFixedModifications
-     * @param getVariableModifications
-     * @return
-     */
     private List<Modification> getModList(MsfFile msfFile, boolean getFixedModifications, boolean getVariableModifications) {
         StringBuilder modNumbersToFetch = new StringBuilder("(");
         List<Modification> modsToReturn = new ArrayList<Modification>();
@@ -274,12 +254,7 @@ private List<Modification> getModList(MsfFile msfFile, boolean getFixedModificat
         return modsToReturn;
     }
 
-    /**
-     *
-     * @param modification
-     * @param aminoAcids
-     * @param msfFile
-     */
+
     private void addAminoAcidsToModification(Modification modification, List<AminoAcid> aminoAcids, MsfFile msfFile) {
         try {
             PreparedStatement stat = null;