import java.awt.dnd.*;\r
import org.biojava.dasobert.eventmodel.*;\r
\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
\r
}\r
\r
+ public AlignViewport getViewport()\r
+ {\r
+ return viewport;\r
+ }\r
+\r
/* Set up intrinsic listeners for dynamically generated GUI bits. */\r
private void addServiceListeners()\r
{\r
{\r
alignPanel.seqPanel.seqCanvas.fr.featuresAdded();\r
alignPanel.repaint();\r
- }\r
- else\r
- {\r
- System.out.println("No Features found for " +\r
- evt.getDasSource().getNickname());\r
+ if(featureSettings!=null)\r
+ featureSettings.setTableData();\r
}\r
}\r
\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
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
new AnnotationExporter().exportFeatures(alignPanel);\r
}\r
\r
+\r
public void exportAnnotations_actionPerformed(ActionEvent e)\r
{\r
new AnnotationExporter().exportAnnotations(\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
return;\r
}\r
\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
-\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
+ SequenceI [] seqs = viewport.getSelectionAsNewSequence();\r
+ String[] omitHidden = null;\r
\r
- Hashtable orderedSeqs = new Hashtable();\r
- SequenceI[] seqs = new SequenceI[sg.getSize()];\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
- {\r
- ch = seq.getCharAt(j);\r
- if (!jalview.util.Comparison.isGap( (ch)))\r
- {\r
- endRes++;\r
- }\r
- }\r
-\r
- if (endRes > 0)\r
+ Vector hiddenColumns = null;\r
+ if(viewport.hasHiddenColumns && viewport.getSelectionGroup()!=null)\r
+ {\r
+ hiddenColumns =new Vector();\r
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
+ for(int i=0; i<viewport.getColumnSelection().getHiddenColumns().size(); i++)\r
{\r
- endRes += seq.getStart() - 1;\r
- }\r
+ int[] region = (int[])\r
+ viewport.getColumnSelection().getHiddenColumns().elementAt(i);\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
- if(seq.getAnnotation()!=null)\r
- {\r
- for(int a=0; a<seq.getAnnotation().length; a++)\r
- seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);\r
+ hiddenColumns.addElement(new int[]{region[0]-hiddenOffset,\r
+ region[1]-hiddenOffset});\r
}\r
}\r
\r
- FastaFile ff = new FastaFile();\r
- ff.addJVSuffix( viewport.showJVSuffix );\r
- c.setContents(new StringSelection( ff.print(seqs)), Desktop.instance);\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
\r
if (newAlignment)\r
{\r
+ System.out.println(format +" 2");\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
else\r
{\r
+ System.out.println(format +" 24");\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
\r
alignment.addSequence(newseq);\r
}\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
AlignFrame af = new AlignFrame(alignment);\r
String newtitle = new String("Copied sequences");\r
\r
+ if(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]+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
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
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
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
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
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.getColumnSelection().revealAllHiddenColumns(viewport);\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
+ alignPanel.repaint();\r
+ }\r
+\r
+ public void hideSelColumns_actionPerformed(ActionEvent e)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ 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
}\r
\r
\r
- public void dbRefs_actionPerformed(ActionEvent e)\r
- {\r
- new DBRefFetcher(viewport.alignment, this);\r
- }\r
-\r
- public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
- {\r
- new DasSequenceFeatureFetcher(viewport.alignment,\r
- this);\r
- viewport.setShowSequenceFeatures(true);\r
- showSeqFeatures.setSelected(true);\r
- }\r
-\r
-\r
+ 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
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
+ tp = new TreePanel(viewport, type, pwType);\r
}\r
\r
addTreeMenuItem(tp, title);\r
SequenceI[] 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
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
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
\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
try{\r
featuresFile = new FeaturesFile(file, type).parse(viewport.alignment.getDataset(),\r
alignPanel.seqPanel.seqCanvas.\r
- getFeatureRenderer().featureColours);\r
+ getFeatureRenderer().featureColours,\r
+ false);\r
}\r
catch(Exception ex)\r
{\r
AppletFormatAdapter.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,\r
- format);\r
-\r
- FastaFile ff = new FastaFile();\r
- Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
- c.setContents(new StringSelection(ff.print(sequences)), Desktop.instance);\r
-\r
- this.paste(false);\r
+ String format = new IdentifyFile().Identify(file, FormatAdapter.FILE);\r
+ new FileLoader().LoadFile(viewport, file, FormatAdapter.FILE, format);\r
}\r
}\r
else\r
git://source.jalview.org / jalview.git / blobdiff