import MCview.*;\r
\r
import jalview.analysis.*;\r
-\r
import jalview.datamodel.*;\r
-\r
-\r
import jalview.schemes.*;\r
+import jalview.commands.ChangeCaseCommand;\r
\r
import java.awt.*;\r
import java.awt.event.*;\r
JMenuItem enterPDB = new JMenuItem();\r
JMenuItem discoverPDB = new JMenuItem();\r
JMenu outputMenu = new JMenu();\r
+ JMenuItem sequenceFeature = new JMenuItem();\r
\r
/**\r
* Creates a new PopupMenu object.\r
\r
if (seq != null)\r
{\r
- int start = Math.max(sequence.getName().length()-15, 0);\r
- sequenceMenu.setText(sequence.getName().substring(start));\r
+ sequenceMenu.setText(sequence.getName());\r
\r
JMenuItem menuItem;\r
if( seq.getDatasetSequence().getPDBId() != null)\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- upperCase_actionPerformed(e);\r
+ changeCase(e);\r
}\r
});\r
copy.setText("Copy");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- lowerCase_actionPerformed(e);\r
+ changeCase(e);\r
}\r
});\r
toggle.setText("Toggle Case");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- toggle_actionPerformed(e);\r
+ changeCase(e);\r
}\r
});\r
pdbMenu.setText("Associate Structure with Sequence");\r
}\r
});\r
outputMenu.setText("Output to Textbox...");\r
+ sequenceFeature.setText("Create Sequence Feature");\r
+ sequenceFeature.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ sequenceFeature_actionPerformed(e);\r
+ }\r
+ });\r
add(groupMenu);\r
\r
add(sequenceMenu);\r
groupMenu.add(editMenu);\r
groupMenu.add(outputMenu);\r
groupMenu.addSeparator();\r
+ groupMenu.add(sequenceFeature);\r
+ groupMenu.addSeparator();\r
groupMenu.add(groupName);\r
groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
+ groupMenu.add(colourMenu);\r
groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
+ groupMenu.add(showText);\r
+ groupMenu.add(showColourText);\r
groupMenu.add(outline);\r
- sequenceMenu.add(sequenceName);\r
+ sequenceMenu.add(sequenceName);\r
sequenceMenu.add(pdbMenu);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
\r
if (abovePIDColour.isSelected())\r
{\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(true), sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
getGroup().getName());\r
\r
sg.cs = udc;\r
}\r
+ refresh();\r
}\r
/**\r
* DOCUMENT ME!\r
{\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
refresh();\r
}\r
\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
refresh();\r
}\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth());\r
+ sg.getSequences(true),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
\r
c.calculate();\r
c.verdict(false, ap.av.ConsPercGaps);\r
groupName.setText(reply);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
-\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for (int i = 0; i < sg.getSize(false); i++)\r
- {\r
- Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);\r
- sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
- sb.append("\n");\r
- }\r
-\r
- sb.append("Something amazing will happen soon");\r
- cap.setText(sb.toString());\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
}\r
\r
s = s.replace(' ', '_');\r
- sequence.getDatasetSequence().setName(s);\r
sequence.setName(s);\r
ap.repaint();\r
}\r
\r
- sequence.getDatasetSequence().setDescription(description.getText());\r
sequence.setDescription(description.getText());\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
}\r
\r
/**\r
ap.alignFrame.cut_actionPerformed(null);\r
}\r
\r
- public void upperCase_actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e.getSource());\r
- }\r
-\r
- public void lowerCase_actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e.getSource());\r
- }\r
-\r
- public void toggle_actionPerformed(ActionEvent e)\r
- {\r
- changeCase(e.getSource());\r
- }\r
-\r
- void changeCase(Object source)\r
+ void changeCase(ActionEvent e)\r
{\r
+ Object source = e.getSource();\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
+ Vector regions = new Vector();\r
if (sg != null)\r
{\r
- for (int g = 0; g < sg.getSize(true); g++)\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
+\r
+ do\r
{\r
- int start = sg.getStartRes();\r
- int end = sg.getEndRes() + 1;\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ if(start==0)\r
+ start = ap.av.colSel.adjustForHiddenColumns(start);\r
+\r
+ end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+ if (start == end)\r
+ end = sg.getEndRes() + 1;\r
+ if (end > sg.getEndRes())\r
+ end = sg.getEndRes() + 1;\r
+ }\r
+\r
+ regions.addElement(new int[]\r
+ {start, end});\r
\r
- do\r
+ if (ap.av.hasHiddenColumns)\r
{\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- end = ap.av.colSel.getHiddenBoundaryRight(start);\r
- if (start == end)\r
- end = sg.getEndRes() + 1;\r
- if (end > sg.getEndRes())\r
- end = sg.getEndRes() + 1;\r
- }\r
+ start = ap.av.colSel.adjustForHiddenColumns(end);\r
+ start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
+ }\r
+ }\r
+ while (end < sg.getEndRes());\r
\r
- if (source == toggle)\r
- ( (SequenceI) sg.getSequences(true).elementAt(g))\r
- .toggleCase(start, end);\r
- else\r
- ( (SequenceI) sg.getSequences(true).elementAt(g))\r
- .changeCase(source == upperCase, start, end);\r
+ int[][] startEnd = new int[regions.size()][2];\r
+ for (int i = 0; i < regions.size(); i++)\r
+ {\r
+ startEnd[i] = (int[]) regions.elementAt(i);\r
+ }\r
\r
- if (ap.av.hasHiddenColumns)\r
- {\r
- start = ap.av.colSel.adjustForHiddenColumns(end);\r
- start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
- }\r
\r
- }\r
- while (end < sg.getEndRes());\r
+ String description;\r
+ int caseChange;\r
+\r
+ if(source==toggle)\r
+ {\r
+ description = "Toggle Case";\r
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
+ }\r
+ else if(source==upperCase)\r
+ {\r
+ description = "To Upper Case";\r
+ caseChange = ChangeCaseCommand.TO_UPPER;\r
+ }\r
+ else\r
+ {\r
+ description = "To Lower Case";\r
+ caseChange = ChangeCaseCommand.TO_LOWER;\r
}\r
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
+\r
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
+ description, sg.getSequencesAsArray(true), startEnd, caseChange\r
+ );\r
+\r
+ ap.alignFrame.addHistoryItem(caseCommand);\r
+\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
}\r
}\r
\r
public void outputText_actionPerformed(ActionEvent e)\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput(null);\r
Desktop.addInternalFrame(cap,\r
"Alignment output - " + e.getActionCommand(), 600,\r
500);\r
new jalview.io.DBRefFetcher(\r
ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
}\r
+\r
+ public void sequenceFeature_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg==null)\r
+ return;\r
+\r
+ int gSize= sg.getSize(false);\r
+ SequenceI [] seqs = new SequenceI[gSize];\r
+ SequenceFeature [] features = new SequenceFeature[gSize];\r
+\r
+ for (int i = 0; i < gSize; i++)\r
+ {\r
+ seqs[i] = sg.getSequenceAt(i).getDatasetSequence();\r
+ int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());\r
+ int end = sg.findEndRes(sg.getSequenceAt(i));\r
+ features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");\r
+ }\r
+\r
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer()\r
+ .createNewFeatures(seqs, features))\r
+ {\r
+ ap.alignFrame.showSeqFeatures.setSelected(true);\r
+ ap.av.setShowSequenceFeatures(true);\r
+ ap.highlightSearchResults(null);\r
+ }\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff