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Merge pull request #130 from tcarver/master

misc
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2 parents 5099f75 + a9906a8 commit 4f43d828974ab9f0198a9ab01f9b11e8bf1cf403 tcarver committed Mar 21, 2013
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23 ChangeLog
@@ -1,5 +1,28 @@
Version XX
+ Add validation checks. This will check the following:
+ All file types:
+ - CDS have no internal stop codon
+ - CDS have valid stop codon
+ GFF / Chado:
+ - check complete gene model
+ - check boundaries are valid
+ - check all features are on the same strand
+ - check CDS features have a phase
+ - check attribute column
+ - qualifiers have a value (not empty)
+ - only reserved tags start with uppercase
+
+ Validation can be run in two ways:
+ 1. using the option in View->Feature Filters->Validation checks... which shows
+ 'failed' features in feature list windows
+ 2. selecting 'Validation report ...' option in the popup menu when right clicking
+ on the feature display. This produces a report with an option to auto-fix gene
+ boundaries and stop codons.
+
+
+Version 15
+
Multiple BAM panels can be opened using the bamClone flag this is used with
the -Dbam flag:
art -Dbam='/pathToFile/file1.bam,/pathToFile/file2.bam' -DbamClone=n
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3 art
@@ -104,6 +104,9 @@ OPTIONS
-Dbam=FILE[,FILE2,...] Open one or more BAM, VCF or BCF files
-DbamClone=n Open all BAMs in multiple (n > 1) panels
-Dbam[1,2,..]=FILE[,FILE2,..] Open BAMs in separate panels
+ -Dshow_snps Show SNP marks in BamView
+ -Dshow_snp_plot Open SNP plot in BamView
+ -Dshow_cov_plot Open coverage plot in BamView
-Dshow_forward_lines=? Hide/show forward frame lines [true,false]
-Dshow_reverse_lines=? Hide/show reverse frame lines [true,false]
-Dchado="h:p/d?u" Get Artemis to open this CHADO database
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4 etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 15.0.1
-ACT Release 12.0.1
+Artemis Release 15.0.2
+ACT Release 12.0.2
DNAPlotter Release 1.10
BamView 1.2.8
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14 uk/ac/sanger/artemis/components/ViewMenu.java
@@ -144,8 +144,8 @@ public void actionPerformed(ActionEvent event)
}
});
- final JMenu view_bases = new JMenu("Bases");
- final JMenuItem view_bases_item = new JMenuItem("Of Selection");
+ final SelectionSubMenu view_bases = new SelectionSubMenu(this, "Bases");
+ final JMenuItem view_bases_item = new JMenuItem("Bases Of Selection");
view_bases_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -156,7 +156,7 @@ public void actionPerformed(ActionEvent event)
view_bases.add(view_bases_item);
final JMenuItem view_bases_as_fasta_item =
- new JMenuItem("Of Selection As FASTA");
+ new JMenuItem("Bases Of Selection As FASTA");
view_bases_as_fasta_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -168,7 +168,7 @@ public void actionPerformed(ActionEvent event)
view_bases.addSeparator();
final JMenuItem view_exon_bases =
- new JMenuItem("Of Selected Exons As FASTA");
+ new JMenuItem("Bases Of Selected Exons As FASTA");
view_exon_bases.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -178,8 +178,8 @@ public void actionPerformed(ActionEvent event)
});
view_bases.add(view_exon_bases);
- final JMenu view_aa = new JMenu("Amino Acids");
- final JMenuItem view_aa_item = new JMenuItem("Of Selection");
+ final SelectionSubMenu view_aa = new SelectionSubMenu(this, "Amino Acids");
+ final JMenuItem view_aa_item = new JMenuItem("Amino Acids Of Selection");
view_aa_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -190,7 +190,7 @@ public void actionPerformed(ActionEvent event)
view_aa.add(view_aa_item);
final JMenuItem view_aa_as_fasta_item =
- new JMenuItem("Of Selection As FASTA");
+ new JMenuItem("Amino Acids Of Selection As FASTA");
view_aa_as_fasta_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
View
22 uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -279,7 +279,7 @@ public BamView(List<String> bamList,
containerPanel.setLayout(new BoxLayout(containerPanel, BoxLayout.Y_AXIS));
containerPanel.add(mainPanel);
-
+
// filter out unmapped reads by default
setSamRecordFlagPredicate(
new SAMRecordFlagPredicate(SAMRecordFlagPredicate.READ_UNMAPPED_FLAG));
@@ -369,6 +369,20 @@ public BamView(List<String> bamList,
jspView.getVerticalScrollBar().setUnitIncrement(8);
addBamToPanel(frame);
+
+ // apply command line options
+ if(System.getProperty("show_snps") != null)
+ isSNPs = true;
+ if(System.getProperty("show_snp_plot") != null)
+ {
+ isSNPplot = true;
+ snpPanel.setVisible(isSNPplot);
+ }
+ if(System.getProperty("show_cov_plot") != null)
+ {
+ isCoverage = true;
+ coveragePanel.setVisible(isCoverage);
+ }
}
public String getToolTipText()
@@ -2658,7 +2672,7 @@ public void actionPerformed(ActionEvent e)
menu.add(viewMenu);
- final JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNP marks");
+ final JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNP marks", isSNPs);
//
JMenu colourMenu = new JMenu("Colour By");
colourMenu.add(colourByCoverageColour);
@@ -2733,7 +2747,7 @@ public void actionPerformed(ActionEvent e)
//
JMenu graphMenu = new JMenu("Graph");
- JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage");
+ JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage", isCoverage);
checkBoxCoverage.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
@@ -2751,7 +2765,7 @@ public void actionPerformed(ActionEvent e)
});
graphMenu.add(checkBoxCoverage);
- JCheckBoxMenuItem checkBoxSNP = new JCheckBoxMenuItem("SNP");
+ JCheckBoxMenuItem checkBoxSNP = new JCheckBoxMenuItem("SNP", isSNPplot);
checkBoxSNP.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
View
6 uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
@@ -1056,7 +1056,7 @@ public static char getSymbolFromIndex(final int index)
/**
* The number of amino acid symbols, not including stop codons: 20.
**/
- public final static int amino_acid_symbol_count = 20;
+ //private final static int amino_acid_symbol_count = 20;
public static void setGeneCode()
@@ -1072,8 +1072,8 @@ public static void setGeneCode()
{
for(int i = 0 ; i < 64 ; ++i)
{
- final char new_table_char =
- ((String)(options_file_table.elementAt(i))).charAt(0);
+ final char new_table_char = Character.toUpperCase(
+ ((String)(options_file_table.elementAt(i))).charAt(0));
if(isLegalCodon (new_table_char))
codon_translation_array[i] = new_table_char;

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