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
{\r
new SequenceFetcher(this);\r
}\r
-\r
-\r
/**\r
* DOCUMENT ME!\r
*\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
thread.start();\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
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
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
+ FeatureRenderer fr = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ fr.featureColours = alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours;\r
+\r
if (title.startsWith("Copied sequences"))\r
{\r
newtitle = title;\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
+ 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
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 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 && !viewport.alignment.isNucleotide())\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
+ }\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
}*/\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
*/\r
public boolean parseGroupsFile(String file)\r
{\r
+ String line = null;\r
try\r
{\r
BufferedReader in = new BufferedReader(new FileReader(file));\r
SequenceI seq = null;\r
- String line, type, desc, token;\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
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
+ 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
alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));\r
}\r
\r
- sf = new SequenceFeature(type, desc, "", start, end);\r
+ sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
\r
seq.getDatasetSequence().addSequenceFeature(sf);\r
}\r
}\r
catch (Exception ex)\r
{\r
+ System.out.println(line);\r
ex.printStackTrace();\r
- System.out.println("Error parsing groups file: " + ex);\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
}\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 AnnotationReader().readAnnotationFile(viewport.\r
+ alignment, file);\r
\r
- if(isAnnotation)\r
+ if (!isAnnotation)\r
+ {\r
+ boolean isGroupsFile = parseGroupsFile(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)), this);\r
\r
- alignPanel.addNotify();\r
+ this.paste(false);\r
}\r
}\r
- catch (Exception ex)\r
+\r
+ if (isAnnotation)\r
{\r
- ex.printStackTrace();\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
}\r
- }\r
-}\r
\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff