import jalview.jbgui.*;\r
import jalview.schemes.*;\r
import jalview.ws.*;\r
+import javax.swing.event.AncestorEvent;\r
\r
/**\r
* DOCUMENT ME!\r
else if(sortby.equals("Pairwise Identity"))\r
sortPairwiseMenuItem_actionPerformed(null);\r
\r
- tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\r
+ // remove(tabbedPane);\r
+ getContentPane().add(alignPanel, BorderLayout.CENTER);\r
+\r
+\r
+\r
+ // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\r
\r
///Dataset tab\r
/////////////////////////\r
-\r
if(al.getDataset()==null)\r
{\r
al.setDataset(null);\r
}\r
-\r
- AlignViewport ds = new AlignViewport(al.getDataset(), true);\r
- AlignmentPanel dap = new AlignmentPanel(this, ds);\r
- tabbedPane.add("Dataset", dap);\r
- viewports.add(ds);\r
- alignPanels.add(dap);\r
+ // AlignViewport ds = new AlignViewport(al.getDataset(), true);\r
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ // tabbedPane.add("Dataset", dap);\r
+ // viewports.add(ds);\r
+ // alignPanels.add(dap);\r
/////////////////////////\r
\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
/* Set up intrinsic listeners for dynamically generated GUI bits. */\r
\r
}\r
\r
+ public void setGUINucleotide(boolean nucleotide)\r
+ {\r
+ showTranslation.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
+ {\r
+ calculateMenu.remove(calculateMenu.getItemCount()-2);\r
+ }\r
+ }\r
+\r
\r
/*\r
Added so Castor Mapping file can obtain Jalview Version\r
}\r
\r
viewport.showSequenceFeatures = true;\r
- ((Alignment)viewport.alignment).featuresAdded = true;\r
\r
alignPanel.repaint();\r
\r
}\r
}\r
\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
+ {\r
+ new SequenceFetcher(this);\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
{\r
- new HTMLOutput(viewport);\r
+ new HTMLOutput(viewport,\r
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
}\r
\r
public void createImageMap(File file, String image)\r
}\r
\r
FastaFile ff = new FastaFile();\r
- ff.addDBPrefix( viewport.showDBPrefix );\r
ff.addJVSuffix( viewport.showJVSuffix );\r
c.setContents(new StringSelection( ff.print(seqs)), this);\r
Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};\r
//!newAlignment\r
for (int i = 0; i < sequences.length; i++)\r
{\r
- viewport.alignment.addSequence(sequences[i]);\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
AlignSeq.extractGaps("-. ", sequences[i].getSequence()),\r
sequences[i].getStart(),\r
sequences[i].getEnd());\r
- sequences[i].setDatasetSequence(ds);\r
+ newseq.setDatasetSequence(ds);\r
viewport.alignment.getDataset().addSequence(ds);\r
-\r
-\r
}\r
\r
}\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
alignPanel.annotationPanel.activeRes = null;\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
if(alignPanel.overviewPanel!=null)\r
alignPanel.overviewPanel.updateOverviewImage();\r
\r
- Provenance prov = viewport.alignment.getProvenance();\r
- if(prov == null)\r
- {\r
- prov = new Provenance();\r
- viewport.alignment.setProvenance(prov);\r
- }\r
-\r
- prov.addEntry("Me",\r
- "Edited in Jalview", new java.util.Date(), "myID");\r
-\r
alignPanel.repaint();\r
}\r
\r
alignPanel.repaint();\r
}\r
\r
- public void seqDBRef_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowDBPrefix(seqDBRef.isSelected());\r
-\r
- alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
- alignPanel.repaint();\r
- }\r
-\r
\r
/**\r
* DOCUMENT ME!\r
{\r
viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
\r
- if (viewport.showSequenceFeatures &&\r
- ! ( (Alignment) viewport.alignment.getDataset()).featuresAdded)\r
+ if (viewport.showSequenceFeatures)\r
{\r
- System.out.println("new fetcher");\r
new SequenceFeatureFetcher(viewport.\r
alignment,\r
alignPanel);\r
{\r
addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
HistoryItem.SORT));\r
- AlignmentSorter.sortByID(viewport.getAlignment(), viewport.showDBPrefix);\r
+ AlignmentSorter.sortByID(viewport.getAlignment());\r
alignPanel.repaint();\r
}\r
\r
{\r
SequenceI seq = null;\r
SequenceI[] msa = null;\r
+/*\r
+ if (predictindex==-1) {\r
\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "The alignment contains no columns or residues usable for prediction!",\r
+ "Invalid Alignment Selection", JOptionPane.WARNING_MESSAGE);\r
+ this.\r
+ return;\r
+ }\r
+*/\r
if ( (viewport.getSelectionGroup() != null) &&\r
(viewport.getSelectionGroup().getSize() > 0))\r
{\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();\r
+ SequenceI[] msa = SeqsetUtils.getNonEmptySequenceSet(gatherSeqOrMsaForSecStrPrediction());\r
+ if (msa==null) {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "There are no columns or residues usable for prediction!\n"\r
+ +"There must be valid residues in at least one\n"\r
+ +"of the sequences in the alignment,\n"\r
+ +"or in the currently selected region.",\r
+ "Invalid Input for Secondary Structure Prediction",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ return;\r
+ }\r
+\r
if (msa.length == 1)\r
{\r
// Single Sequence prediction\r
{\r
if (msa.length > 1)\r
{\r
- // Single Sequence prediction\r
+ // Aligned Sequences prediction\r
jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
title, msa);\r
}\r
// TODO: group services by location as well as function.\r
}\r
\r
- public void vamsasStore_actionPerformed(ActionEvent e)\r
+ /* public void vamsasStore_actionPerformed(ActionEvent e)\r
{\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
getProperty("LAST_DIRECTORY"));\r
//vs.store(chooser.getSelectedFile().getAbsolutePath() );\r
vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);\r
}\r
- }\r
+ }*/\r
\r
public void featureSettings_actionPerformed(ActionEvent e)\r
{\r
\r
public void showTranslation_actionPerformed(ActionEvent e)\r
{\r
-\r
- if(!viewport.alignment.isNucleotide())\r
- return;\r
-\r
- viewport.showTranslation(showTranslation.isSelected());\r
-\r
- if(!viewport.alignment.isNucleotide())\r
- return;\r
-\r
int s, sSize = viewport.alignment.getHeight();\r
SequenceI [] newSeq = new SequenceI[sSize];\r
\r
int res, resSize;\r
StringBuffer protein;\r
- SequenceI seq;\r
+ String seq;\r
for(s=0; s<sSize; s++)\r
{\r
protein = new StringBuffer();\r
- seq = (SequenceI)viewport.alignment.getSequenceAt(s);\r
- resSize = seq.getLength();\r
+ seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());\r
+ resSize = seq.length();\r
for(res = 0; res < resSize; res+=3)\r
{\r
- String codon = seq.getSequence(res, res+3);\r
+ String codon = seq.substring(res, res+3);\r
codon = codon.replace('U', 'T');\r
String aa = ResidueProperties.codonTranslate(codon);\r
if(aa==null)\r
else\r
protein.append( aa );\r
}\r
- newSeq[s] = new Sequence(seq.getName(), protein.toString());\r
+ newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());\r
}\r
\r
\r
}\r
\r
\r
- // Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
- // NEW_WINDOW_WIDTH,\r
- // NEW_WINDOW_HEIGHT);\r
+ AlignFrame af = new AlignFrame(al);\r
+ Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
+ NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+\r
\r
- AlignViewport newViewport = new AlignViewport(al);\r
- AlignmentPanel ap = new AlignmentPanel(this, newViewport);\r
- tabbedPane.add("Protein", ap);\r
- viewports.add(newViewport);\r
- alignPanels.add(ap);\r
+ // AlignViewport newViewport = new AlignViewport(al);\r
+ // AlignmentPanel ap = new AlignmentPanel(this, newViewport);\r
+ // tabbedPane.add("Protein", ap);\r
+ // viewports.add(newViewport);\r
+ // alignPanels.add(ap);\r
\r
///Dataset tab\r
/////////////////////////\r
\r
- AlignViewport ds = new AlignViewport(al.getDataset());\r
- ds.setDataset(true);\r
- AlignmentPanel dap = new AlignmentPanel(this, ds);\r
- tabbedPane.add("Dataset", dap);\r
- viewports.add(ds);\r
- alignPanels.add(dap);\r
+ // AlignViewport ds = new AlignViewport(al.getDataset());\r
+ // ds.setDataset(true);\r
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ // tabbedPane.add("Dataset", dap);\r
+ // viewports.add(ds);\r
+ // alignPanels.add(dap);\r
/////////////////////////\r
\r
\r
}\r
\r
-public void tabSelected()\r
-{\r
+/*public void tabSelected()\r
+ {\r
int index = tabbedPane.getSelectedIndex();\r
viewport = (AlignViewport)viewports.elementAt(index);\r
alignPanel = (AlignmentPanel)alignPanels.elementAt(index);\r
-}\r
-\r
+ }*/\r
}\r
git://source.jalview.org / jalview.git / blobdiff