\r
String jalviewServletURL;\r
\r
- TCoffeeScoreFile tcoffeeScoreFile;\r
\r
public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)\r
{\r
changeColour(new Blosum62ColourScheme());\r
}\r
else if (source == tcoffeeColour) {\r
- changeColour(new TCoffeeColourScheme(tcoffeeScoreFile));\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
}\r
else if (source == annotationColour)\r
{\r
{\r
try\r
{\r
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
+ sg.cs = cs.getClass().newInstance();\r
} catch (Exception ex)\r
{\r
ex.printStackTrace();\r
\r
TCoffeeScoreFile file = TCoffeeScoreFile.load( new InputStreamReader( url.openStream() ) );\r
if( file == null ) {\r
++ // TODO: raise a dialog box here rather than bomb out.\r
++ \r
throw new RuntimeException("The file provided does not match the T-Coffee scores file format");\r
}\r
- // TODO add parameter to indicate if matching should be done\r
+ \r
+ /*\r
+ * check that the score matrix matches the alignment dimensions\r
+ */\r
+ AlignmentI aln; \r
+ if( (aln=viewport.alignment) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {\r
- throw new RuntimeException("The scores matrix does not match the alignment dimensions");\r
++ // TODO: raise a dialog box here rather than bomb out.\r
++ throw new RuntimeException("The scores matrix does not match the alignment dimensions");\r
++ \r
+ }\r
+ \r
- tcoffeeColour.setEnabled(true);\r
- tcoffeeScoreFile = file;\r
- \r
- // switch to this color\r
- changeColour(new TCoffeeColourScheme(tcoffeeScoreFile));\r
++ // TODO add parameter to indicate if matching should be done\r
+ if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
+ {\r
+ tcoffeeColour.setEnabled(true);\r
+ // switch to this color\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ }\r
-\r
}\r
\r
\r
Vector alignPanels = new Vector();
- TCoffeeScoreFile tcoffeeScoreFile;
-
/**
* Last format used to load or save alignments in this window
*/
}
FormatAdapter f = new FormatAdapter();
String output = f.formatSequences(format,
- (Alignment) viewport.alignment, // class cast exceptions will
+ viewport.alignment, // class cast exceptions will
// occur in the distant future
omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
{
try
{
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+ sg.cs = cs.getClass().newInstance();
} catch (Exception ex)
{
}
try
{
TCoffeeScoreFile result = TCoffeeScoreFile.load(new File(sFilePath));
- if( result == null ) { throw new RuntimeException("The file provided does not match the T-Coffee scores file format"); }
-
- // TODO check that the loaded scores matches the current MSA 'dimension'
+ if( result == null ) {
++ // TODO: raise a dialog box here rather than bomb out.
++
+ throw new RuntimeException("The file provided does not match the T-Coffee scores file format");
+ }
+
+ /*
+ * check that the score matrix matches the alignment dimensions
+ */
+ AlignmentI aln;
+ if( (aln=viewport.alignment) != null && (aln.getHeight() != result.getHeight() || aln.getWidth() != result.getWidth()) ) {
- throw new RuntimeException("The scores matrix does not match the alignment dimensions");
++ // TODO: raise a dialog box here rather than bomb out.
++ throw new RuntimeException("The scores matrix does not match the alignment dimensions");
+ }
-
- changeColour( new TCoffeeColourScheme(result) );
- tcoffeeScoreFile = result;
- tcoffeeColour.setEnabled(true);
- tcoffeeColour.setSelected(true);
-
+ if (result.annotateAlignment(alignPanel.getAlignment(), true))
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ // switch to this color
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
+ } else {
+ tcoffeeColour.setEnabled(false);
+ tcoffeeColour.setSelected(false);
+ }
}
catch (Exception ex) {
JOptionPane.showMessageDialog(
@Override
protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) {
- if( tcoffeeScoreFile != null ) {
- changeColour( new TCoffeeColourScheme(tcoffeeScoreFile) );
- }
+ changeColour( new TCoffeeColourScheme(alignPanel.getAlignment()) );
}
// /**
package jalview.io;
+ import jalview.analysis.SequenceIdMatcher;
+ import jalview.datamodel.AlignmentAnnotation;
+ import jalview.datamodel.AlignmentI;
+ import jalview.datamodel.Annotation;
+ import jalview.datamodel.SequenceI;
+
+ import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
* insertion order.
*/
LinkedHashMap<String,StringBuilder> scores = new LinkedHashMap<String,StringBuilder>();
-
+
+ Integer fWidth;
/**
* Parse the specified file.
}
/**
+ * @return The 'height' of the score matrix i.e. the numbers of score rows that should matches
+ * the number of sequences in the alignment
+ */
+ public int getHeight() {
+ // the last entry will always be the 'global' alingment consensus scores, so it is removed
+ // from the 'height' count to make this value compatible with the number of sequences in the MSA
+ return scores != null && scores.size() > 0 ? scores.size()-1 : 0;
+ }
+
+ /**
+ * @return The 'width' of the score matrix i.e. the number of columns.
+ * Since teh score value are supposd to be calculated for an 'aligned' MSA, all the entries
+ * have to have the same width.
+ */
+ public int getWidth() {
+ return fWidth != null ? fWidth : 0;
+ }
+
+ /**
* The default constructor is marked as {@code protected} since this class is meant to created
* through the {@link #load(File)} or {@link #load(Reader)} factory methods
*/
for( Map.Entry<String,String> entry : block.items.entrySet() ) {
StringBuilder scoreStringBuilder = scores.get(entry.getKey());
if( scoreStringBuilder == null ) {
- throw new RuntimeException(String.format("Invalid T-Coffee score file. Sequence ID '%s' is not declared in header section", entry.getKey()));
+ throw new RuntimeException(String.format("Invalid T-Coffee score file: Sequence ID '%s' is not declared in header section", entry.getKey()));
}
scoreStringBuilder.append( entry.getValue() );
}
-
}
+ /*
+ * verify that all rows have the same width
+ */
+ for( StringBuilder str : scores.values() ) {
+ if( fWidth == null ) {
+ fWidth = str.length();
+ }
+ else if( fWidth != str.length() ) {
+ throw new RuntimeException("Invalid T-Coffee score file: All the score sequences must have the same length");
+ }
+ }
+
+
+
}
return items.get("cons");
}
}
-
-
+ /**
+ * TCOFFEE score colourscheme
+ */
+ static final Color[] colors = {
+ new Color( 102, 102, 255 ), // #6666FF
+ new Color( 0, 255, 0), // #00FF00
+ new Color( 102, 255, 0), // #66FF00
+ new Color( 204, 255, 0), // #CCFF00
+ new Color( 255, 255, 0), // #FFFF00
+ new Color( 255, 204, 0), // #FFCC00
+ new Color( 255, 153, 0), // #FF9900
+ new Color( 255, 102, 0), // #FF6600
+ new Color( 255, 51, 0), // #FF3300
+ new Color( 255, 34, 0) // #FF2000
+ };
+ public final static String TCOFFEE_SCORE="TCoffeeScore";
+ /**
+ * generate annotation for this TCoffee score set on the given alignment
+ * @param al alignment to annotate
+ * @param matchids if true, annotate sequences based on matching sequence names
+ * @return true if alignment annotation was modified, false otherwise.
+ */
+ public boolean annotateAlignment(AlignmentI al, boolean matchids)
+ {
+ boolean added=false;
+ int i=0;
+ SequenceIdMatcher sidmatcher = new SequenceIdMatcher(al.getSequencesArray());
+ byte[][] scoreMatrix=getScoresArray();
+ // for 2.8 - we locate any existing TCoffee annotation and remove it first before adding this.
+ for (Map.Entry<String,StringBuilder> id:scores.entrySet())
+ {
+ byte[] srow=scoreMatrix[i];
+ SequenceI s;
+ if (matchids)
+ {
+ s=sidmatcher.findIdMatch(id.getKey());
+ } else {
+ s=al.getSequenceAt(i);
+ }
+ i++;
+ if (s==null && i!=scores.size() && !id.getKey().equals("cons"))
+ {
+ System.err.println("No "+(matchids ? "match ":" sequences left ")+" for TCoffee score set : "+id.getKey());
+ continue;
+ }
+ int jSize=al.getWidth()< srow.length ? al.getWidth() : srow.length;
+ Annotation[] annotations=new Annotation[al.getWidth()];
+ for (int j=0;j<jSize;j++) {
+ byte val = srow[j];
+ annotations[j]=new Annotation(s==null ? ""+val:null,s==null ? ""+val:null,(char) val,val*1f,val >= 0 && val < colors.length ? colors[val] : Color.white);
+ }
+ AlignmentAnnotation aa=null;
+ if (s!=null)
+ {
+ // TODO - set per sequence score
+ aa=new AlignmentAnnotation(TCOFFEE_SCORE, "Score for "+id.getKey(), annotations);
+
+ aa.setSequenceRef(s);
+ aa.visible=false;
+ aa.belowAlignment=false;
+ } else {
+ aa=new AlignmentAnnotation("T-COFFEE", "TCoffee column reliability score", annotations);
+ aa.belowAlignment=true;
+ aa.visible=true;
+
+ }
+ al.addAnnotation(aa);
+ added=true;
+ }
+ return added;
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff