* @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
{\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
*\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
\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
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
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
- //>>>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
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
*\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
\r
public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
{\r
- if (!viewport.alignment.isNucleotide())\r
- {\r
- new SequenceFeatureFetcher(viewport.\r
- alignment,\r
- alignPanel);\r
+ new DasSequenceFeatureFetcher(viewport.\r
+ alignment,\r
+ alignPanel);\r
viewport.setShowSequenceFeatures(true);\r
showSeqFeatures.setSelected(true);\r
- }\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
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
- String line = null;\r
- try\r
- {\r
- BufferedReader in = new BufferedReader(new FileReader(file));\r
- SequenceI seq = null;\r
- String type, desc, token;\r
-\r
- int index, start, end;\r
- StringTokenizer st;\r
- SequenceFeature sf;\r
- int lineNo = 0;\r
- String featureGroup = null;\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
- if (type.equalsIgnoreCase("startgroup"))\r
- {\r
- featureGroup = st.nextToken();\r
- }\r
- else if (type.equalsIgnoreCase("endgroup"))\r
- {\r
- //We should check whether this is the current group,\r
- //but at present theres no way of showing more than 1 group\r
- st.nextToken();\r
- featureGroup = null;\r
- }\r
- else\r
- {\r
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type,\r
- ucs.findColour("A"));\r
- }\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
-\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, featureGroup);\r
-\r
- seq.getDatasetSequence().addSequenceFeature(sf);\r
- }\r
- }\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
+ catch(Exception ex)\r
{\r
- System.out.println(line);\r
ex.printStackTrace();\r
- System.out.println("Error parsing groups file: " + ex +"\n"+line);\r
- return false;\r
}\r
\r
- viewport.showSequenceFeatures = true;\r
- showSeqFeatures.setSelected(true);\r
- alignPanel.repaint();\r
- return true;\r
+ if(featuresFile)\r
+ {\r
+ viewport.showSequenceFeatures = true;\r
+ showSeqFeatures.setSelected(true);\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ return featuresFile;\r
}\r
\r
public void dragEnter(DropTargetDragEvent evt)\r
public void loadJalviewDataFile(String file)\r
{\r
try{\r
- boolean isAnnotation = new AnnotationReader().readAnnotationFile(viewport.\r
+ boolean isAnnotation = new AnnotationFile().readAnnotationFile(viewport.\r
alignment, file);\r
\r
if (!isAnnotation)\r
{\r
- boolean isGroupsFile = parseGroupsFile(file);\r
+ boolean isGroupsFile = parseFeaturesFile(file,\r
+ AppletFormatAdapter.FILE);\r
if (!isGroupsFile)\r
{\r
String protocol = "File";\r
\r
FastaFile ff = new FastaFile();\r
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- c.setContents(new StringSelection(ff.print(sequences)), this);\r
+ c.setContents(new StringSelection(ff.print(sequences)), Desktop.instance);\r
\r
this.paste(false);\r
}\r
}\r
-\r
- if (isAnnotation)\r
+ else\r
{\r
- int height = alignPanel.annotationPanel.adjustPanelHeight();\r
- alignPanel.annotationScroller.setPreferredSize(\r
- new Dimension(alignPanel.annotationScroller.getWidth(),\r
- height));\r
-\r
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(new Dimension(\r
- alignPanel.annotationSpaceFillerHolder.getWidth(),\r
- height));\r
-\r
- alignPanel.addNotify();\r
+ // (isAnnotation)\r
+ alignPanel.adjustAnnotationHeight();\r
}\r
\r
}catch(Exception ex)\r
git://source.jalview.org / jalview.git / blobdiff