* @version $Revision$\r
*/\r
public class AlignFrame\r
- extends GAlignFrame implements ClipboardOwner, DropTargetListener\r
+ extends GAlignFrame implements DropTargetListener\r
{\r
/** DOCUMENT ME!! */\r
public static final int NEW_WINDOW_WIDTH = 700;\r
AlignmentPanel alignPanel;\r
AlignViewport viewport;\r
\r
- Vector viewports = new Vector();\r
- Vector alignPanels = new Vector();\r
-\r
/** DOCUMENT ME!! */\r
public String currentFileFormat = null;\r
Stack historyList = new Stack();\r
public AlignFrame(AlignmentI al)\r
{\r
viewport = new AlignViewport(al);\r
- viewports.add(viewport);\r
\r
this.setDropTarget(new java.awt.dnd.DropTarget(this, this));\r
\r
}\r
\r
alignPanel = new AlignmentPanel(this, viewport);\r
- alignPanels.add(alignPanel);\r
\r
String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");\r
\r
});\r
\r
\r
- if (Desktop.desktop != null)\r
- {\r
- addServiceListeners();\r
- setGUINucleotide(al.isNucleotide());\r
- }\r
+ if (Desktop.desktop != null)\r
+ {\r
+ addServiceListeners();\r
+ setGUINucleotide(al.isNucleotide());\r
+ }\r
+\r
+ if(jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))\r
+ {\r
+ wrapMenuItem.setSelected(true);\r
+ wrapMenuItem_actionPerformed(null);\r
+ }\r
}\r
\r
/* Set up intrinsic listeners for dynamically generated GUI bits. */\r
public void setGUINucleotide(boolean nucleotide)\r
{\r
showTranslation.setVisible( nucleotide );\r
- sequenceFeatures.setVisible(!nucleotide );\r
- featureSettings.setVisible( !nucleotide );\r
+ //sequenceFeatures.setVisible(!nucleotide );\r
+ //featureSettings.setVisible( !nucleotide );\r
conservationMenuItem.setVisible( !nucleotide );\r
modifyConservation.setVisible( !nucleotide );\r
\r
- //Deal with separators\r
//Remember AlignFrame always starts as protein\r
- if(nucleotide)\r
- {\r
- viewMenu.remove(viewMenu.getItemCount()-2);\r
- }\r
- else\r
+ if(!nucleotide)\r
{\r
calculateMenu.remove(calculateMenu.getItemCount()-2);\r
}\r
return jalview.bin.Cache.getProperty("VERSION");\r
}\r
\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ }\r
+\r
\r
public void fetchSequence_actionPerformed(ActionEvent e)\r
{\r
new SequenceFetcher(this);\r
}\r
\r
+ public void addFromFile_actionPerformed(ActionEvent e)\r
+ {\r
+ Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);\r
+ }\r
+\r
+ public void addFromText_actionPerformed(ActionEvent e)\r
+ {\r
+ Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);\r
+ }\r
+\r
+ public void addFromURL_actionPerformed(ActionEvent e)\r
+ {\r
+ Desktop.instance.inputURLMenuItem_actionPerformed(viewport);\r
+ }\r
\r
/**\r
* DOCUMENT ME!\r
public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
{\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty(\r
- "LAST_DIRECTORY"),\r
+ getProperty( "LAST_DIRECTORY"),\r
new String[]\r
- {\r
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
- "jar"\r
- },\r
+ { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc","jar" },\r
new String[]\r
- {\r
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
- }, currentFileFormat);\r
+ { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },\r
+ currentFileFormat,\r
+ false);\r
+\r
\r
- chooser.setAcceptAllFileFilterUsed(false);\r
chooser.setFileView(new JalviewFileView());\r
chooser.setDialogTitle("Save Alignment to file");\r
chooser.setToolTipText("Save");\r
java.io.File.separatorChar) + 1);\r
}\r
\r
- Jalview2XML.SaveAlignment(this, file, shortName);\r
+ new Jalview2XML().SaveAlignment(this, file, shortName);\r
\r
// USE Jalview2XML to save this file\r
return true;\r
\r
out.print(output);\r
out.close();\r
+ this.setTitle(file);\r
return true;\r
}\r
catch (Exception ex)\r
thread.start();\r
}\r
\r
+ public void exportFeatures_actionPerformed(ActionEvent e)\r
+ {\r
+ new AnnotationExporter().exportFeatures(alignPanel);\r
+ }\r
+\r
+ public void exportAnnotations_actionPerformed(ActionEvent e)\r
+ {\r
+ new AnnotationExporter().exportAnnotations(\r
+ alignPanel,\r
+ viewport.alignment.getAlignmentAnnotation()\r
+ );\r
+ }\r
+\r
+\r
+ public void associatedData_actionPerformed(ActionEvent e)\r
+ {\r
+ // Pick the tree file\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"));\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Load Jalview Annotations or Features File");\r
+ chooser.setToolTipText("Load Jalview Annotations / Features file");\r
+\r
+ int value = chooser.showOpenDialog(null);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ loadJalviewDataFile(choice);\r
+ }\r
+\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
// used by undo and redo\r
void restoreHistoryItem(HistoryItem hi)\r
{\r
- if (hi.getType() == HistoryItem.SORT)\r
- {\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
- {\r
- viewport.alignment.getSequences().setElementAt(hi.getSequences()\r
- .elementAt(i),\r
- i);\r
- }\r
- }\r
- else\r
- {\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
- {\r
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
-\r
- if (restore.getLength() == 0)\r
- {\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- viewport.alignment.getSequences().insertElementAt(restore,\r
- hi.getAlignIndex(i));\r
- }\r
- else\r
- {\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- }\r
- }\r
\r
- if (hi.getType() == HistoryItem.PASTE)\r
- {\r
- for (int i = viewport.alignment.getHeight() - 1;\r
- i > (hi.getSequences().size() - 1); i--)\r
- {\r
- viewport.alignment.deleteSequence(i);\r
- }\r
- }\r
- }\r
+ hi.restore();\r
\r
updateEditMenuBar();\r
\r
alignPanel.repaint();\r
}\r
\r
- public void lostOwnership(Clipboard clipboard, Transferable contents)\r
- {\r
- Desktop.jalviewClipboard = null;\r
- }\r
\r
\r
/**\r
seqs[i].setDBRef(seq.getDBRef());\r
seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
-\r
+ if(seq.getAnnotation()!=null)\r
+ {\r
+ for(int a=0; a<seq.getAnnotation().length; a++)\r
+ seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);\r
+ }\r
}\r
\r
FastaFile ff = new FastaFile();\r
ff.addJVSuffix( viewport.showJVSuffix );\r
- c.setContents(new StringSelection( ff.print(seqs)), this);\r
+ c.setContents(new StringSelection( ff.print(seqs)), Desktop.instance);\r
Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};\r
}\r
\r
if(str.length()<1)\r
return;\r
\r
- String format = IdentifyFile.Identify(str, "Paste");\r
+ String format = new IdentifyFile().Identify(str, "Paste");\r
SequenceI[] sequences;\r
\r
if(Desktop.jalviewClipboard!=null)\r
sequences = new FormatAdapter().readFile(str, "Paste", format);\r
}\r
\r
+ AlignmentI alignment = null;\r
+\r
if (newAlignment)\r
{\r
-\r
- Alignment alignment = new Alignment(sequences);\r
+ alignment = new Alignment(sequences);\r
\r
if(Desktop.jalviewClipboard!=null)\r
alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
else\r
alignment.setDataset( null );\r
-\r
-\r
- AlignFrame af = new AlignFrame(alignment);\r
- String newtitle = new String("Copied sequences");\r
-\r
- if (title.startsWith("Copied sequences"))\r
- {\r
- newtitle = title;\r
- }\r
- else\r
- {\r
- newtitle = newtitle.concat("- from " + title);\r
- }\r
-\r
- Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
- NEW_WINDOW_HEIGHT);\r
}\r
else\r
{\r
+ alignment = viewport.getAlignment();\r
+\r
//!newAlignment\r
for (int i = 0; i < sequences.length; i++)\r
{\r
+\r
Sequence newseq = new Sequence(sequences[i].getName(),\r
sequences[i].getSequence(), sequences[i].getStart(),\r
sequences[i].getEnd());\r
- viewport.alignment.addSequence(newseq);\r
- if(sequences[i].getDatasetSequence()==null)\r
- {\r
- ////////////////////////////\r
- //Datset needs extension;\r
- /////////////////////////////\r
- Sequence ds = new Sequence(sequences[i].getName(),\r
- AlignSeq.extractGaps("-. ", sequences[i].getSequence()),\r
- sequences[i].getStart(),\r
- sequences[i].getEnd());\r
- newseq.setDatasetSequence(ds);\r
- viewport.alignment.getDataset().addSequence(ds);\r
- }\r
- else\r
- {\r
- newseq.setDatasetSequence(sequences[i].getDatasetSequence());\r
- if(sequences[i].getDatasetSequence().getAnnotation()!=null)\r
- {\r
- for(int aa=0; aa<sequences[i].getDatasetSequence().getAnnotation().length; aa++)\r
- {\r
- viewport.alignment.addAnnotation(sequences[i].getDatasetSequence().getAnnotation()[aa]);\r
- }\r
- }\r
- }\r
+\r
+ alignment.addSequence(newseq);\r
}\r
- viewport.setEndSeq(viewport.alignment.getHeight());\r
- viewport.alignment.getWidth();\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ viewport.setEndSeq(alignment.getHeight());\r
+ alignment.getWidth();\r
+ viewport.firePropertyChange("alignment", null, alignment.getSequences());\r
}\r
+\r
+ // Add any annotations attached to sequences\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ if (sequences[i].getAnnotation() != null)\r
+ {\r
+ for (int a = 0; a < sequences[i].getAnnotation().length; a++)\r
+ {\r
+ AlignmentAnnotation newAnnot =\r
+ new AlignmentAnnotation(\r
+ sequences[i].getAnnotation()[a].label,\r
+ sequences[i].getAnnotation()[a].description,\r
+ sequences[i].getAnnotation()[a].annotations,\r
+ sequences[i].getAnnotation()[a].graphMin,\r
+ sequences[i].getAnnotation()[a].graphMax,\r
+ sequences[i].getAnnotation()[a].graph);\r
+\r
+ sequences[i].getAnnotation()[a] = newAnnot;\r
+ newAnnot.sequenceMapping = sequences[i].getAnnotation()[a].\r
+ sequenceMapping;\r
+ newAnnot.sequenceRef = sequences[i];\r
+ newAnnot.adjustForAlignment();\r
+ alignment.addAnnotation(newAnnot);\r
+ alignment.setAnnotationIndex(newAnnot, a);\r
+ }\r
+\r
+ alignPanel.annotationPanel.adjustPanelHeight();\r
+ }\r
+ }\r
+\r
+ if(newAlignment)\r
+ {\r
+ AlignFrame af = new AlignFrame(alignment);\r
+ String newtitle = new String("Copied sequences");\r
+\r
+\r
+ //>>>This is a fix for the moment, until a better solution is found!!<<<\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
+\r
+\r
+ if (title.startsWith("Copied sequences"))\r
+ {\r
+ newtitle = title;\r
+ }\r
+ else\r
+ {\r
+ newtitle = newtitle.concat("- from " + title);\r
+ }\r
+\r
+ Desktop.addInternalFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+\r
+ }\r
+\r
+\r
}\r
catch (Exception ex)\r
{\r
return;\r
}\r
\r
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
- HistoryItem.HIDE));\r
\r
SequenceGroup sg = viewport.getSelectionGroup();\r
- boolean allSequences = false;\r
- if (sg.sequences.size() == viewport.alignment.getHeight())\r
+\r
+\r
+\r
+ //Jalview no longer allows deletion of residues.\r
+ //Check here whether any residues are in selection area\r
+ /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
{\r
- allSequences = true;\r
- }\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int j = sg.getStartRes();\r
+ do\r
+ {\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(\r
+ Desktop.desktop, "Cannot delete residues from alignment!\n"\r
+ + "Try hiding columns instead.",\r
+ "Deletion of residues not permitted",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+ j++;\r
+ }while(j<=sg.getEndRes());\r
+ }\r
+ }*/\r
+\r
+\r
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
\r
for (int i = 0; i < sg.sequences.size(); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.getAlignment().findIndex(seq);\r
+\r
seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
\r
// If the cut affects all sequences, remove highlighted columns\r
- if (allSequences)\r
+ if (sg.sequences.size() == viewport.alignment.getHeight())\r
{\r
viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
sg.getEndRes() + 1);\r
*/\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ if(viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.keyboardNo1 = null;\r
+ alignPanel.seqPanel.keyboardNo2 = null;\r
+ }\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
alignPanel.idPanel.idCanvas.searchResults = null;\r
- alignPanel.annotationPanel.activeRes = null;\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
\r
public void alignmentChanged()\r
{\r
- if(viewport.vconsensus!=null)\r
+ if(viewport.padGaps)\r
+ viewport.getAlignment().padGaps();\r
+\r
+ if(viewport.vconsensus!=null && viewport.autoCalculateConsensus)\r
{\r
viewport.updateConsensus();\r
viewport.updateConservation();\r
{\r
addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
HistoryItem.HIDE));\r
- if (viewport.getAlignment().padGaps())\r
- alignmentChanged();\r
+\r
+ viewport.padGaps = padGapsMenuitem.isSelected();\r
+\r
+ // if (viewport.padGaps)\r
+ alignmentChanged();\r
}\r
\r
/**\r
JInternalFrame frame = new JInternalFrame();\r
Finder finder = new Finder(viewport, alignPanel, frame);\r
frame.setContentPane(finder);\r
- Desktop.addInternalFrame(frame, "Find", 340, 110);\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ Desktop.addInternalFrame(frame, "Find", 340, 110);\r
}\r
\r
/**\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ public void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
+ {\r
+ new DasSequenceFeatureFetcher(viewport.\r
+ alignment,\r
+ alignPanel);\r
+ viewport.setShowSequenceFeatures(true);\r
+ showSeqFeatures.setSelected(true);\r
+ }\r
+\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+ new FeatureSettings(viewport, alignPanel);\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @param evt DOCUMENT ME!\r
*/\r
- public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
+ public void showSeqFeatures_actionPerformed(ActionEvent evt)\r
{\r
- viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
-\r
- if (viewport.showSequenceFeatures)\r
+ viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());\r
+ alignPanel.repaint();\r
+ if (alignPanel.getOverviewPanel() != null)\r
{\r
- new SequenceFeatureFetcher(viewport.\r
- alignment,\r
- alignPanel);\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
}\r
-\r
- featureSettings.setEnabled(true);\r
-\r
- alignPanel.repaint();\r
}\r
\r
/**\r
new PCAPanel(viewport);\r
}\r
\r
+\r
+ public void autoCalculate_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.autoCalculateConsensus = autoCalculate.isSelected();\r
+ if(viewport.autoCalculateConsensus)\r
+ {\r
+ alignmentChanged();\r
+ }\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
void NewTreePanel(String type, String pwType, String title)\r
{\r
- final TreePanel tp;\r
+ TreePanel tp;\r
\r
if ( (viewport.getSelectionGroup() != null) &&\r
(viewport.getSelectionGroup().getSize() > 3))\r
}\r
\r
addTreeMenuItem(tp, title);\r
- viewport.setCurrentTree(tp.getTree());\r
\r
Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
}\r
{\r
// Add any Multiple Sequence Alignment Services\r
final JMenu msawsmenu = new JMenu("Alignment");\r
+ final AlignFrame af = this;\r
for (int i = 0, j = msaws.size(); i < j; i++)\r
{\r
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
- false, true, viewport.getAlignment().getDataset());\r
+ false, true, viewport.getAlignment().getDataset(), af);\r
\r
}\r
\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
- true, true, viewport.getAlignment().getDataset());\r
+ true, true, viewport.getAlignment().getDataset(), af);\r
\r
}\r
\r
}\r
}*/\r
\r
- public void featureSettings_actionPerformed(ActionEvent e)\r
- {\r
- new FeatureSettings(viewport, alignPanel);\r
- }\r
+\r
\r
\r
\r
protein = new StringBuffer();\r
seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());\r
resSize = seq.length();\r
+ resSize -= resSize%3;\r
+\r
for(res = 0; res < resSize; res+=3)\r
{\r
String codon = seq.substring(res, res+3);\r
jalview.datamodel.AlignmentAnnotation[] annotations\r
= viewport.alignment.getAlignmentAnnotation();\r
int a, aSize;\r
- for (int i = 0; i < annotations.length; i++)\r
+ if(annotations!=null)\r
{\r
-\r
- if (annotations[i].label.equals("Quality") ||\r
- annotations[i].label.equals("Conservation") ||\r
- annotations[i].label.equals("Consensus"))\r
+ for (int i = 0; i < annotations.length; i++)\r
{\r
- continue;\r
- }\r
-\r
+ if (annotations[i].label.equals("Quality") ||\r
+ annotations[i].label.equals("Conservation") ||\r
+ annotations[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
\r
- aSize = viewport.alignment.getWidth()/3;\r
- jalview.datamodel.Annotation [] anots =\r
- new jalview.datamodel.Annotation[aSize];\r
+ aSize = viewport.alignment.getWidth() / 3;\r
+ jalview.datamodel.Annotation[] anots =\r
+ new jalview.datamodel.Annotation[aSize];\r
\r
- for(a=0; a<viewport.alignment.getWidth(); a++)\r
- {\r
- if( annotations[i].annotations[a]==null\r
- || annotations[i].annotations[a]==null)\r
- continue;\r
+ for (a = 0; a < viewport.alignment.getWidth(); a++)\r
+ {\r
+ if (annotations[i].annotations[a] == null\r
+ || annotations[i].annotations[a] == null)\r
+ continue;\r
\r
- anots[a/3] = new Annotation(\r
- annotations[i].annotations[a].displayCharacter,\r
- annotations[i].annotations[a].description,\r
- annotations[i].annotations[a].secondaryStructure,\r
- annotations[i].annotations[a].value,\r
- annotations[i].annotations[a].colour);\r
- }\r
+ anots[a / 3] = new Annotation(\r
+ annotations[i].annotations[a].displayCharacter,\r
+ annotations[i].annotations[a].description,\r
+ annotations[i].annotations[a].secondaryStructure,\r
+ annotations[i].annotations[a].value,\r
+ annotations[i].annotations[a].colour);\r
+ }\r
\r
- jalview.datamodel.AlignmentAnnotation aa\r
+ jalview.datamodel.AlignmentAnnotation aa\r
= new jalview.datamodel.AlignmentAnnotation(annotations[i].label,\r
- annotations[i].description, anots );\r
- al.addAnnotation(aa);\r
+ annotations[i].description, anots);\r
+ al.addAnnotation(aa);\r
+ }\r
}\r
\r
-\r
AlignFrame af = new AlignFrame(al);\r
Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
NEW_WINDOW_WIDTH,\r
*\r
* @param String DOCUMENT ME!\r
*/\r
-public boolean parseGroupsFile(String file)\r
+public boolean parseFeaturesFile(String file, String type)\r
{\r
- try\r
+ boolean featuresFile = false;\r
+ try{\r
+ featuresFile = new FeaturesFile(file, type).parse(viewport.alignment,\r
+ alignPanel.seqPanel.seqCanvas.\r
+ getFeatureRenderer().featureColours);\r
+ }\r
+ catch(Exception ex)\r
{\r
- BufferedReader in = new BufferedReader(new FileReader(file));\r
- SequenceI seq = null;\r
- String line, type, desc, token;\r
-\r
- int index, start, end;\r
- StringTokenizer st;\r
- SequenceFeature sf;\r
- int lineNo = 0;\r
- while ( (line = in.readLine()) != null)\r
- {\r
- lineNo++;\r
- st = new StringTokenizer(line, "\t");\r
- if (st.countTokens() == 2)\r
- {\r
- type = st.nextToken();\r
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));\r
- continue;\r
- }\r
-\r
- while (st.hasMoreElements())\r
- {\r
- desc = st.nextToken();\r
- token = st.nextToken();\r
- if (!token.equals("ID_NOT_SPECIFIED"))\r
- {\r
- index = viewport.alignment.findIndex(viewport.alignment.findName(token));\r
- st.nextToken();\r
- }\r
- else\r
- {\r
- index = Integer.parseInt(st.nextToken());\r
- }\r
-\r
- start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
-\r
- seq = viewport.alignment.getSequenceAt(index);\r
- start = seq.findIndex(start) - 1;\r
- end = seq.findIndex(end) - 1;\r
-\r
- type = st.nextToken();\r
-\r
- if (alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type) == null)\r
- {\r
- // Probably the old style groups file\r
- UserColourScheme ucs = new UserColourScheme(type);\r
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));\r
- }\r
-\r
- sf = new SequenceFeature(type, desc, "", start, end);\r
-\r
- seq.getDatasetSequence().addSequenceFeature(sf);\r
- }\r
- }\r
+ ex.printStackTrace();\r
}\r
- catch (Exception ex)\r
+\r
+ if(featuresFile)\r
{\r
- System.out.println("Error parsing groups file: " + ex);\r
- return false;\r
+ viewport.showSequenceFeatures = true;\r
+ showSeqFeatures.setSelected(true);\r
+ alignPanel.repaint();\r
}\r
\r
- viewport.showSequenceFeatures = true;\r
- alignPanel.repaint();\r
- return true;\r
+ return featuresFile;\r
}\r
\r
public void dragEnter(DropTargetDragEvent evt)\r
{\r
e.printStackTrace();\r
}\r
-\r
if (files != null)\r
{\r
try\r
{\r
- boolean isAnnotation = false;\r
\r
for (int i = 0; i < files.size(); i++)\r
{\r
- String file = files.get(i).toString();\r
-\r
- isAnnotation = new AnnotationReader().readAnnotationFile(viewport.alignment, file);\r
-\r
- if( !isAnnotation )\r
- {\r
- boolean isGroupsFile = parseGroupsFile(file);\r
- if (!isGroupsFile)\r
- {\r
- String protocol = "File";\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
- SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);\r
-\r
- FastaFile ff = new FastaFile();\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- c.setContents(new StringSelection(ff.print(sequences)), this);\r
-\r
- this.paste(false);\r
-\r
- }\r
- }\r
+ loadJalviewDataFile(files.get(i).toString());\r
}\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+}\r
+\r
+ // This method will attempt to load a "dropped" file first by testing\r
+ // whether its and Annotation file, then features file. If both are\r
+ // false then the user may have dropped an alignment file onto this\r
+ // AlignFrame\r
+ public void loadJalviewDataFile(String file)\r
+ {\r
+ try{\r
+ boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.\r
+ alignment, file);\r
\r
- if(isAnnotation)\r
+ if (!isAnnotation)\r
+ {\r
+ boolean isGroupsFile = parseFeaturesFile(file,\r
+ AppletFormatAdapter.FILE);\r
+ if (!isGroupsFile)\r
{\r
- int height = alignPanel.annotationPanel.adjustPanelHeight();\r
- alignPanel.annotationScroller.setPreferredSize(\r
- new Dimension(alignPanel.annotationScroller.getWidth(),\r
- height));\r
+ String protocol = "File";\r
+ String format = new IdentifyFile().Identify(file, protocol);\r
+ SequenceI[] sequences = new FormatAdapter().readFile(file, protocol,\r
+ format);\r
\r
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
- alignPanel.annotationSpaceFillerHolder.getWidth(),\r
- height));\r
+ FastaFile ff = new FastaFile();\r
+ Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ c.setContents(new StringSelection(ff.print(sequences)), Desktop.instance);\r
\r
- alignPanel.addNotify();\r
+ this.paste(false);\r
}\r
}\r
- catch (Exception ex)\r
+ else\r
{\r
- ex.printStackTrace();\r
+ // (isAnnotation)\r
+ alignPanel.adjustAnnotationHeight();\r
}\r
- }\r
-}\r
\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff