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
\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
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
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
}\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
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\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
+\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