showSeqFeatures.setSelected(av.showSequenceFeatures);
hiddenMarkers.setState(av.showHiddenMarkers);
- applyToAllGroups.setState(av.colourAppliesToAllGroups);
+ applyToAllGroups.setState(av.getColourAppliesToAllGroups());
showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
showDbRefsMenuitem.setSelected(av.isShowDbRefs());
autoCalculate.setSelected(av.autoCalculateConsensus);
{
if (fileName != null)
{
+ // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+ // originating file's format
// TODO: work out how to recover feature settings for correct view(s) when
// file is reloaded.
if (currentFileFormat.equals("Jalview"))
synchronized void slideSequences(boolean right, int size)
{
- Vector sg = new Vector();
+ List<SequenceI> sg = new Vector();
if (viewport.cursorMode)
{
- sg.addElement(viewport.getAlignment().getSequenceAt(
+ sg.add(viewport.getAlignment().getSequenceAt(
alignPanel.seqPanel.seqCanvas.cursorY));
}
else if (viewport.getSelectionGroup() != null
invertGroup.add(viewport.getAlignment().getSequenceAt(i));
}
- SequenceI[] seqs1 = new SequenceI[sg.size()];
- for (int i = 0; i < sg.size(); i++)
- seqs1[i] = (SequenceI) sg.elementAt(i);
-
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
+
SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
for (int i = 0; i < invertGroup.size(); i++)
seqs2[i] = (SequenceI) invertGroup.elementAt(i);
addHistoryItem(trimRegion);
- Vector groups = viewport.getAlignment().getGroups();
-
- for (int i = 0; i < groups.size(); i++)
+ for (SequenceGroup sg :viewport.getAlignment().getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.get(i);
-
if ((trimLeft && !sg.adjustForRemoveLeft(column))
|| (!trimLeft && !sg.adjustForRemoveRight(column)))
{
*/
public void clustalColour_actionPerformed(ActionEvent e)
{
- changeColour(new ClustalxColourScheme(viewport.getAlignment()
- .getSequences(), viewport.getAlignment().getWidth()));
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences()));
}
/**
if (viewport.getColourAppliesToAllGroups())
{
- Vector groups = viewport.getAlignment().getGroups();
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ for (SequenceGroup sg:viewport.getAlignment().getGroups())
+ {
if (cs == null)
{
sg.cs = null;
if (cs instanceof ClustalxColourScheme)
{
- sg.cs = new ClustalxColourScheme(sg.getSequences(viewport
- .getHiddenRepSequences()), sg.getWidth());
+ sg.cs = new ClustalxColourScheme(sg, viewport
+ .getHiddenRepSequences());
}
else if (cs instanceof UserColourScheme)
{
return;
}
- int s = 0;
SequenceGroup sg = viewport.getSelectionGroup();
/* Decide if the selection is a column region */
- while (s < sg.getSize())
+ for (SequenceI _s:sg.getSequences())
{
- if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg
+ if (_s.getLength() < sg
.getEndRes())
{
JOptionPane
}
}
}
-
- @Override
- public void loadScores_actionPerformed(ActionEvent e)
- {
- // Pick the tree file
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select a T-Coffee scores ascii file");
- chooser.setToolTipText("Load a score file");
-
- int value = chooser.showOpenDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- String sFilePath = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", sFilePath);
-
-
- try
- {
- TCoffeeScoreFile result = new TCoffeeScoreFile(sFilePath, FormatAdapter.FILE);
- if (!result.isValid()) {
- JOptionPane.showMessageDialog(Desktop.desktop, result.getWarningMessage(),
- "Problem reading T-COFFEE score file", JOptionPane.WARNING_MESSAGE);
- return;
- }
-
- /*
- * check that the score matrix matches the alignment dimensions
- */
- AlignmentI aln;
- if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != result.getHeight() || aln.getWidth() != result.getWidth()) ) {
- // TODO: raise a dialog box here rather than bomb out.
- JOptionPane.showMessageDialog(Desktop.desktop, "The scores matrix does not match the alignment dimensions",
- "Problem reading T-COFFEE score file", JOptionPane.WARNING_MESSAGE);
- }
- 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);
- }
- if (result.getWarningMessage()!=null)
- {
- JOptionPane.showMessageDialog(Desktop.desktop, result.getWarningMessage(),"Problem reading T-COFEEE score file", JOptionPane.WARNING_MESSAGE);
- }
- }
- catch (Exception ex) {
- JOptionPane.showMessageDialog(
- Desktop.desktop,
- ex.getMessage(),
- "unexpected problem reading T-COFFEE score file",
- JOptionPane.WARNING_MESSAGE);
-
- ex.printStackTrace();
- }
- }
-
- }
-
@Override
- protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) {
- changeColour( new TCoffeeColourScheme(alignPanel.getAlignment()) );
+ protected void tcoffeeColorScheme_actionPerformed(ActionEvent e)
+ {
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
}
-
-// /**
-// * Load the (T-Coffee) score file from the specified url
-// *
-// * @param url The absolute path from where download and read the score file
-// * @throws IOException
-// */
-// public void loadScoreFile(URL url ) throws IOException {
-//
-// TCoffeeScoreFile result = new TCoffeeScoreFile();
-// result.parse( new InputStreamReader( url.openStream() ) );
-// tcoffeeScoreFile = result;
-// }
-
+
public TreePanel ShowNewickTree(NewickFile nf, String title)
{
return ShowNewickTree(nf, title, 600, 500, 4, 5);
if (!isAnnotation)
{
- // try to see if its a JNet 'concise' style annotation file *before* we
- // try to parse it as a features file
- if (format == null)
+ // first see if its a T-COFFEE score file
+ TCoffeeScoreFile tcf = null;
+ try
{
- format = new IdentifyFile().Identify(file, protocol);
- }
- if (format.equalsIgnoreCase("JnetFile"))
+ tcf = new TCoffeeScoreFile(file, protocol);
+ if (tcf.isValid())
+ {
+ if (tcf.annotateAlignment(viewport.getAlignment(), true))
+ {
+ tcoffeeColour.setEnabled(true);
+ tcoffeeColour.setSelected(true);
+ changeColour(new TCoffeeColourScheme(viewport.getAlignment()));
+ isAnnotation = true;
+ statusBar
+ .setText("Successfully pasted T-Coffee scores to alignment.");
+ }
+ else
+ {
+ // some problem - if no warning its probable that the ID matching process didn't work
+ JOptionPane.showMessageDialog(Desktop.desktop,
+ tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(),
+ "Problem reading T-COFFEE score file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ else
+ {
+ tcf = null;
+ }
+ } catch (Exception x)
{
- jalview.io.JPredFile predictions = new jalview.io.JPredFile(file,
- protocol);
- new JnetAnnotationMaker().add_annotation(predictions,
- viewport.getAlignment(), 0, false);
- isAnnotation = true;
+ Cache.log.debug("Exception when processing data source as T-COFFEE score file",x);
+ tcf = null;
}
- else
+ if (tcf == null)
{
- /*
- * if (format.equalsIgnoreCase("PDB")) {
- *
- * String pdbfn = ""; // try to match up filename with sequence id try
- * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new
- * File(file); pdbfn = fl.getName(); } else if (protocol ==
- * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
- * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null)
- * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
- * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { //
- * attempt to find a match in the alignment SequenceI mtch =
- * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
- * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l)
- * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch =
- * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate
- * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
- * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) {
- * System.err.println("Associated file : " + file + " with " +
- * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
- * TODO: maybe need to load as normal otherwise return; } }
- */
+ // try to see if its a JNet 'concise' style annotation file *before*
+ // we
// try to parse it as a features file
- boolean isGroupsFile = parseFeaturesFile(file, protocol);
- // if it wasn't a features file then we just treat it as a general
- // alignment file to load into the current view.
- if (!isGroupsFile)
+ if (format == null)
{
- new FileLoader().LoadFile(viewport, file, protocol, format);
+ format = new IdentifyFile().Identify(file, protocol);
+ }
+ if (format.equalsIgnoreCase("JnetFile"))
+ {
+ jalview.io.JPredFile predictions = new jalview.io.JPredFile(
+ file, protocol);
+ new JnetAnnotationMaker().add_annotation(predictions,
+ viewport.getAlignment(), 0, false);
+ isAnnotation = true;
}
else
{
- alignPanel.paintAlignment(true);
+ /*
+ * if (format.equalsIgnoreCase("PDB")) {
+ *
+ * String pdbfn = ""; // try to match up filename with sequence id
+ * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
+ * new File(file); pdbfn = fl.getName(); } else if (protocol ==
+ * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
+ * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
+ * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+ * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
+ * // attempt to find a match in the alignment SequenceI mtch =
+ * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while
+ * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) >
+ * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch
+ * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and
+ * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq()
+ * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null)
+ * { System.err.println("Associated file : " + file + " with " +
+ * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } //
+ * TODO: maybe need to load as normal otherwise return; } }
+ */
+ // try to parse it as a features file
+ boolean isGroupsFile = parseFeaturesFile(file, protocol);
+ // if it wasn't a features file then we just treat it as a general
+ // alignment file to load into the current view.
+ if (!isGroupsFile)
+ {
+ new FileLoader().LoadFile(viewport, file, protocol, format);
+ }
+ else
+ {
+ alignPanel.paintAlignment(true);
+ }
}
}
}
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
col = col.brighter();
- for (Enumeration sq = gps[g].getSequences(null).elements(); sq
- .hasMoreElements(); viewport.setSequenceColour(
- (SequenceI) sq.nextElement(), col))
+ for (SequenceI s:gps[g].getSequences())
+ viewport.setSequenceColour(
+ s, col)
;
}
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
git://source.jalview.org / jalview.git / blobdiff