import jalview.schemes.*;\r
import jalview.ws.*;\r
import java.awt.dnd.*;\r
-\r
+import org.biojava.dasobert.eventmodel.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @version $Revision$\r
*/\r
public class AlignFrame\r
- extends GAlignFrame implements ClipboardOwner, DropTargetListener\r
+ extends GAlignFrame implements DropTargetListener, FeatureListener\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
Stack redoList = new Stack();\r
private int treeCount = 0;\r
\r
-\r
/**\r
- * Creates a new AlignFrame object.\r
- *\r
- * @param al DOCUMENT ME!\r
+ * new alignment window with hidden columns\r
+ * @param al AlignmentI\r
+ * @param hiddenColumns ColumnSelection or null\r
*/\r
- public AlignFrame(AlignmentI al)\r
- {\r
- viewport = new AlignViewport(al);\r
- viewports.add(viewport);\r
+ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns) {\r
+\r
+ viewport = new AlignViewport(al, hiddenColumns);\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
+ if (Desktop.desktop != null)\r
+ {\r
+ addServiceListeners();\r
+ setGUINucleotide(al.isNucleotide());\r
+ }\r
+\r
+\r
+ if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))\r
+ {\r
+ wrapMenuItem.setSelected(true);\r
+ wrapMenuItem_actionPerformed(null);\r
+ }\r
+\r
+ }\r
+\r
+\r
+ /**\r
+ * Creates a new AlignFrame object.\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ */\r
+ public AlignFrame(AlignmentI al)\r
{\r
- addServiceListeners();\r
- setGUINucleotide(al.isNucleotide());\r
+ this(al, null);\r
}\r
+\r
+ public AlignViewport getViewport()\r
+ {\r
+ return viewport;\r
}\r
\r
/* Set up intrinsic listeners for dynamically generated GUI bits. */\r
}\r
;\r
});\r
-\r
}\r
\r
public void setGUINucleotide(boolean nucleotide)\r
}\r
}\r
\r
+ public void comeBackLater(FeatureEvent evt)\r
+ {}\r
+\r
+ public void newFeatures(FeatureEvent evt)\r
+ {\r
+ if (evt.getFeatures().length > 0)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas.fr.featuresAdded();\r
+ alignPanel.repaint();\r
+ }\r
+ }\r
+\r
+ Hashtable progressBars;\r
+ public void setProgressBar(String message, long id)\r
+ {\r
+ if(progressBars == null)\r
+ progressBars = new Hashtable();\r
+\r
+ JPanel progressPanel;\r
+ GridLayout layout = (GridLayout) statusPanel.getLayout();\r
+ if(progressBars.get( new Long(id) )!=null)\r
+ {\r
+ progressPanel = (JPanel)progressBars.get( new Long(id) );\r
+ statusPanel.remove(progressPanel);\r
+ progressBars.remove( progressPanel );\r
+ progressPanel = null;\r
+ if(message!=null)\r
+ statusBar.setText(message);\r
+\r
+ layout.setRows(layout.getRows() - 1);\r
+ }\r
+ else\r
+ {\r
+ progressPanel = new JPanel(new BorderLayout(10, 5));\r
+\r
+ JProgressBar progressBar = new JProgressBar();\r
+ progressBar.setIndeterminate(true);\r
+\r
+ progressPanel.add(new JLabel(message), BorderLayout.WEST);\r
+ progressPanel.add(progressBar, BorderLayout.CENTER);\r
+\r
+ layout.setRows(layout.getRows() + 1);\r
+ statusPanel.add(progressPanel);\r
+\r
+ progressBars.put(new Long(id), progressPanel);\r
+ }\r
+\r
+ validate();\r
+ }\r
+\r
\r
/*\r
Added so Castor Mapping file can obtain Jalview Version\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
*\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
else\r
{\r
- String output = new FormatAdapter().formatSequences(format,\r
- viewport.getAlignment().\r
- getSequences());\r
+\r
+ String[] omitHidden = null;\r
+\r
+ if (viewport.hasHiddenColumns)\r
+ {\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ "The Alignment contains hidden columns."\r
+ + "\nDo you want to save only the visible alignment?",\r
+ "Save / Omit Hidden Columns",\r
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (reply == JOptionPane.YES_OPTION)\r
+ omitHidden = viewport.getViewAsString(false);\r
+ }\r
+\r
+ String output = new FormatAdapter().formatSequences(\r
+ format,\r
+ viewport.alignment.getSequencesArray(),\r
+ omitHidden);\r
+\r
if (output == null)\r
{\r
return false;\r
\r
out.print(output);\r
out.close();\r
+ this.setTitle(file);\r
return true;\r
}\r
catch (Exception ex)\r
*/\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
+ String [] omitHidden = null;\r
+\r
+ if(viewport.hasHiddenColumns)\r
+ {\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ "The Alignment contains hidden columns."\r
+ +"\nDo you want to output only the visible alignment?",\r
+ "Save / Omit Hidden Columns",\r
+ JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if(reply==JOptionPane.YES_OPTION)\r
+ {\r
+ omitHidden = viewport.getViewAsString(false);\r
+ }\r
+ }\r
+\r
CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
Desktop.addInternalFrame(cap,\r
"Alignment output - " + e.getActionCommand(), 600,\r
500);\r
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
- viewport.getAlignment().\r
- getSequences()));\r
+\r
+\r
+ cap.setText(new FormatAdapter().formatSequences(\r
+ e.getActionCommand(),\r
+ viewport.alignment.getSequencesArray(),\r
+ omitHidden));\r
}\r
\r
/**\r
thread.start();\r
}\r
\r
+ public void exportFeatures_actionPerformed(ActionEvent e)\r
+ {\r
+ new AnnotationExporter().exportFeatures(alignPanel);\r
+ }\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
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(false).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(false).contains(temp))\r
{\r
continue;\r
}\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(false).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(false).contains(temp))\r
{\r
continue;\r
}\r
alignPanel.repaint();\r
}\r
\r
- public void lostOwnership(Clipboard clipboard, Transferable contents)\r
- {\r
- Desktop.jalviewClipboard = null;\r
- }\r
\r
\r
/**\r
return;\r
}\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
-\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
-\r
- Hashtable orderedSeqs = new Hashtable();\r
- SequenceI[] seqs = new SequenceI[sg.getSize()];\r
+ SequenceI [] seqs = viewport.getSelectionAsNewSequence();\r
+ String[] omitHidden = null;\r
\r
- for (int i = 0; i < sg.getSize(); i++)\r
+ if (viewport.hasHiddenColumns)\r
{\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.alignment.findIndex(seq);\r
- orderedSeqs.put(index + "", seq);\r
+ omitHidden = viewport.getViewAsString(true);\r
}\r
\r
- int index = 0, startRes, endRes;\r
- char ch;\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI seq = null;\r
-\r
- while (seq == null)\r
- {\r
- if (orderedSeqs.containsKey(index + ""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
-\r
- break;\r
- }\r
- else\r
- {\r
- index++;\r
- }\r
- }\r
+ String output = new FormatAdapter().formatSequences(\r
+ "Fasta",\r
+ seqs,\r
+ omitHidden);\r
\r
- //FIND START RES\r
- //Returns residue following index if gap\r
- startRes = seq.findPosition(sg.getStartRes());\r
\r
- //FIND END RES\r
- //Need to find the residue preceeding index if gap\r
- endRes = 0;\r
+ Toolkit.getDefaultToolkit().getSystemClipboard()\r
+ .setContents(new StringSelection(output), Desktop.instance);\r
\r
- for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
+ Vector hiddenColumns = null;\r
+ if(viewport.hasHiddenColumns)\r
+ {\r
+ hiddenColumns =new Vector();\r
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
+ for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)\r
{\r
- ch = seq.getCharAt(j);\r
- if (!jalview.util.Comparison.isGap( (ch)))\r
- {\r
- endRes++;\r
- }\r
- }\r
+ int[] region = (int[])\r
+ viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
\r
- if (endRes > 0)\r
- {\r
- endRes += seq.getStart() - 1;\r
+ hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,\r
+ region[1]-hiddenOffset});\r
}\r
-\r
- seqs[i] = new Sequence(seq.getName(),\r
- seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),\r
- startRes,\r
- endRes);\r
- seqs[i].setDescription(seq.getDescription());\r
- seqs[i].setDBRef(seq.getDBRef());\r
- seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
- seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
-\r
}\r
\r
- FastaFile ff = new FastaFile();\r
- ff.addJVSuffix( viewport.showJVSuffix );\r
- c.setContents(new StringSelection( ff.print(seqs)), this);\r
- Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};\r
+ Desktop.jalviewClipboard = new Object[]{ seqs,\r
+ viewport.alignment.getDataset(),\r
+ hiddenColumns};\r
}\r
\r
/**\r
String format = new IdentifyFile().Identify(str, "Paste");\r
SequenceI[] sequences;\r
\r
+\r
if(Desktop.jalviewClipboard!=null)\r
{\r
// The clipboard was filled from within Jalview, we must use the sequences\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
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
+\r
+\r
+ viewport.setEndSeq(alignment.getHeight());\r
+ alignment.getWidth();\r
+ viewport.firePropertyChange("alignment", null, alignment.getSequences());\r
}\r
+\r
+\r
+\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
+ if(Desktop.jalviewClipboard!=null && Desktop.jalviewClipboard[2]!=null)\r
+ {\r
+ Vector hc = (Vector)Desktop.jalviewClipboard[2];\r
+ for(int i=0; i<hc.size(); i++)\r
+ {\r
+ int [] region = (int[]) hc.elementAt(i);\r
+ af.viewport.hideColumns(region[0], region[1]);\r
+ }\r
+ }\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
//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
+ /* if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
{\r
for (int i = 0; i < sg.sequences.size(); i++)\r
{\r
j++;\r
}while(j<=sg.getEndRes());\r
}\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
+ for (int i = 0; i < sg.getSize(false); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.getAlignment().findIndex(seq);\r
seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
\r
// If the cut affects all sequences, remove highlighted columns\r
- if (sg.sequences.size() == viewport.alignment.getHeight())\r
+ if (sg.getSize(false) == 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.repaint();\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
+ public void invertColSel_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
int end = viewport.alignment.getWidth();\r
\r
if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().sequences != null\r
- && viewport.getSelectionGroup().sequences.size() > 0)\r
+ && viewport.getSelectionGroup().getSequences(true) != null\r
+ && viewport.getSelectionGroup().getSize(true) > 0)\r
{\r
- seqs = viewport.getSelectionGroup().sequences;\r
+ seqs = viewport.getSelectionGroup().getSequences(true);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes()+1;\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
SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
{\r
- ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+ ((ClustalxColourScheme)sg.cs).resetClustalX(\r
+ sg.getSequences(true), sg.getWidth());\r
}\r
sg.recalcConservation();\r
}\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
*\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
scaleAbove.setVisible(wrapMenuItem.isSelected());\r
scaleLeft.setVisible(wrapMenuItem.isSelected());\r
scaleRight.setVisible(wrapMenuItem.isSelected());\r
+ viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
+ alignPanel.setWrapAlignment(wrapMenuItem.isSelected());\r
+ }\r
+\r
+ public void showAllSeqs_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ repaint();\r
+ }\r
+\r
+ public void showAllColumns_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ }\r
+\r
+ public void hideSelSequences_actionPerformed(ActionEvent e)\r
+ {\r
+ if(viewport.getSelectionGroup()==null)\r
+ return;\r
+\r
+ SequenceI [] seqs = viewport.getSelectionGroup().getSequencesInOrder(\r
+ viewport.alignment\r
+ );\r
+\r
+ for(int i=0; i<seqs.length; i++)\r
+ {\r
+ viewport.hideSequence(seqs[i]);\r
+ }\r
+\r
alignPanel.repaint();\r
}\r
\r
+ public void hideSelColumns_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void hiddenMarkers_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());\r
+ repaint();\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
alignPanel.repaint();\r
}\r
\r
- public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
- {\r
- if (!viewport.alignment.isNucleotide())\r
- {\r
- new SequenceFeatureFetcher(viewport.\r
- alignment,\r
- alignPanel);\r
- viewport.setShowSequenceFeatures(true);\r
- showSeqFeatures.setSelected(true);\r
- }\r
- }\r
-\r
\r
+ public FeatureSettings featureSettings;\r
public void featureSettings_actionPerformed(ActionEvent e)\r
{\r
- new FeatureSettings(viewport, alignPanel);\r
+ if(featureSettings !=null )\r
+ {\r
+ featureSettings.close();\r
+ featureSettings = null;\r
+ }\r
+ featureSettings = new FeatureSettings(this);\r
}\r
\r
/**\r
*\r
* @param cs DOCUMENT ME!\r
*/\r
- void changeColour(ColourSchemeI cs)\r
+ public void changeColour(ColourSchemeI cs)\r
{\r
int threshold = 0;\r
\r
\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ sg.cs = new ClustalxColourScheme(\r
+ sg.getSequences(true), sg.getWidth());\r
}\r
else if (cs instanceof UserColourScheme)\r
{\r
sg.cs.setThreshold(threshold,\r
viewport.getIgnoreGapsConsensus());\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- sg.getWidth()));\r
- }\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(true), 0,\r
+ sg.getWidth()));\r
+ }\r
else\r
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
+ sg.getSequences(true), 0,\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
*/\r
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
{\r
- RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(sp);\r
- Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400,\r
- 100, false);\r
+ new RedundancyPanel(alignPanel, this);\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
{\r
if ( (viewport.getSelectionGroup() == null) ||\r
- (viewport.getSelectionGroup().getSize() < 2))\r
+ (viewport.getSelectionGroup().getSize(false) < 2))\r
{\r
JOptionPane.showInternalMessageDialog(this,\r
"You must select at least 2 sequences.",\r
public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
if ( ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() < 4) &&\r
- (viewport.getSelectionGroup().getSize() > 0)) ||\r
+ (viewport.getSelectionGroup().getSize(false) < 4) &&\r
+ (viewport.getSelectionGroup().getSize(false) > 0)) ||\r
(viewport.getAlignment().getHeight() < 4))\r
{\r
JOptionPane.showInternalMessageDialog(this,\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
+ (viewport.getSelectionGroup().getSize(false) > 3))\r
{\r
int s = 0;\r
SequenceGroup sg = viewport.getSelectionGroup();\r
\r
/* Decide if the selection is a column region */\r
- while (s < sg.sequences.size())\r
+ while (s < sg.getSize(false))\r
{\r
- if ( ( (SequenceI) sg.sequences.elementAt(s++)).getLength() <\r
+ if ( ( (SequenceI) sg.getSequences(false).elementAt(s++)).getLength() <\r
sg.getEndRes())\r
{\r
JOptionPane.showMessageDialog(Desktop.desktop,\r
}\r
\r
title = title + " on region";\r
- tp = new TreePanel(viewport,\r
- viewport.getSelectionGroup().sequences, type, pwType,\r
- sg.getStartRes(), sg.getEndRes());\r
+ tp = new TreePanel(viewport, type, pwType);\r
}\r
else\r
{\r
return;\r
}\r
\r
- tp = new TreePanel(viewport,\r
- viewport.getAlignment().getSequences(), type, pwType,\r
- 0,\r
- viewport.alignment.getWidth());\r
+ if(viewport.alignment.getHeight()<2)\r
+ return;\r
+\r
+ tp = new TreePanel(viewport, type, pwType);\r
}\r
\r
addTreeMenuItem(tp, title);\r
- viewport.setCurrentTree(tp.getTree());\r
\r
Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
}\r
* or just the selected set will be submitted for multiple alignment.\r
*\r
*/\r
- private SequenceI[] gatherSequencesForAlignment()\r
+ private jalview.datamodel.AlignmentView gatherSequencesForAlignment()\r
{\r
// Now, check we have enough sequences\r
- SequenceI[] msa = null;\r
+ AlignmentView msa = null;\r
\r
if ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 1))\r
+ (viewport.getSelectionGroup().getSize(false) > 1))\r
{\r
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
+ /*SequenceGroup seqs = viewport.getSelectionGroup();\r
int sz;\r
- msa = new SequenceI[sz = seqs.getSize()];\r
+ msa = new SequenceI[sz = seqs.getSize(false)];\r
\r
for (int i = 0; i < sz; i++)\r
{\r
msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
+ } */\r
+ msa = viewport.getAlignmentView(true);\r
}\r
else\r
{\r
- Vector seqs = viewport.getAlignment().getSequences();\r
+ /*Vector seqs = viewport.getAlignment().getSequences();\r
\r
if (seqs.size() > 1)\r
{\r
{\r
msa[i] = (SequenceI) seqs.elementAt(i);\r
}\r
- }\r
+ }*/\r
+ msa = viewport.getAlignmentView(false);\r
}\r
return msa;\r
}\r
SequenceI[] msa = null;\r
\r
if ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 0))\r
+ (viewport.getSelectionGroup().getSize(false) > 0))\r
{\r
// JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
SequenceGroup seqs = viewport.getSelectionGroup();\r
\r
- if ( (seqs.getSize() == 1) || !viewport.alignment.isAligned())\r
+ if ( (seqs.getSize(false) == 1) || !viewport.alignment.isAligned())\r
{\r
seq = (SequenceI) seqs.getSequenceAt(0);\r
}\r
else\r
{\r
int sz;\r
- msa = new SequenceI[sz = seqs.getSize()];\r
+ msa = new SequenceI[sz = seqs.getSize(false)];\r
\r
for (int i = 0; i < sz; i++)\r
{\r
if (nf.getTree() != null)\r
{\r
tp = new TreePanel(viewport,\r
- viewport.getAlignment().getSequences(), nf,\r
"FromFile",\r
- title);\r
+ title,\r
+ nf);\r
\r
tp.setSize(w,h);\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
public void actionPerformed(ActionEvent e)\r
{\r
- SequenceI[] msa = gatherSequencesForAlignment();\r
+ AlignmentView 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
public void actionPerformed(ActionEvent e)\r
{\r
- SequenceI[] msa = gatherSequencesForAlignment();\r
+ AlignmentView 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
-\r
public void showTranslation_actionPerformed(ActionEvent e)\r
{\r
- int s, sSize = viewport.alignment.getHeight();\r
+ SequenceI [] selection = viewport.getSelectionAsNewSequence();\r
+ String [] seqstring = viewport.getViewAsString(true);\r
+\r
+ int s, sSize = selection.length;\r
SequenceI [] newSeq = new SequenceI[sSize];\r
\r
int res, resSize;\r
for(s=0; s<sSize; s++)\r
{\r
protein = new StringBuffer();\r
- seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());\r
+ seq = AlignSeq.extractGaps("-. ", seqstring[s]);\r
resSize = seq.length();\r
resSize -= resSize%3;\r
\r
else\r
protein.append( aa );\r
}\r
- newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());\r
+ newSeq[s] = new Sequence(selection[s].getName(),\r
+ protein.toString());\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);\r
- sf.setFeatureGroup(featureGroup);\r
-\r
- seq.getDatasetSequence().addSequenceFeature(sf);\r
- }\r
- }\r
+ boolean featuresFile = false;\r
+ try{\r
+ featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),\r
+ alignPanel.seqPanel.seqCanvas.\r
+ getFeatureRenderer().featureColours,\r
+ false);\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
{\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 = new 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
- }\r
-\r
- if(isAnnotation)\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
+ loadJalviewDataFile(files.get(i).toString());\r
}\r
}\r
catch (Exception ex)\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
+ {\r
+ boolean isGroupsFile = parseFeaturesFile(file,\r
+ AppletFormatAdapter.FILE);\r
+ if (!isGroupsFile)\r
+ {\r
+ String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);\r
+ new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ // (isAnnotation)\r
+ alignPanel.adjustAnnotationHeight();\r
+ }\r
+\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff