/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
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
+ JMenuItem textColour = new JMenuItem();\r
+ JMenu jMenu1 = new JMenu();\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
add(menuItem);\r
\r
if(ap.av.getSelectionGroup() !=null\r
- && ap.av.getSelectionGroup().getSize(false)>1)\r
+ && ap.av.getSelectionGroup().getSize()>1)\r
{\r
menuItem = new JMenuItem("Represent Group with " + seq.getName());\r
menuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupName_actionPerformed(e);\r
+ groupName_actionPerformed();\r
}\r
});\r
sequenceMenu.setText("Sequence");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- sequenceName_actionPerformed(e);\r
+ sequenceName_actionPerformed();\r
}\r
});\r
PIDColour.setFocusPainted(false);\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- unGroupMenuItem_actionPerformed(e);\r
+ unGroupMenuItem_actionPerformed();\r
}\r
});\r
\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- outline_actionPerformed(e);\r
+ outline_actionPerformed();\r
}\r
});\r
nucleotideMenuItem.setText("Nucleotide");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- nucleotideMenuItem_actionPerformed(e);\r
+ nucleotideMenuItem_actionPerformed();\r
}\r
});\r
colourMenu.setText("Group Colour");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- showBoxes_actionPerformed(e);\r
+ showBoxes_actionPerformed();\r
}\r
});\r
showText.setText("Text");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- showText_actionPerformed(e);\r
+ showText_actionPerformed();\r
}\r
});\r
showColourText.setText("Colour Text");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- showColourText_actionPerformed(e);\r
+ showColourText_actionPerformed();\r
}\r
});\r
editMenu.setText("Edit");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- cut_actionPerformed(e);\r
+ cut_actionPerformed();\r
}\r
});\r
upperCase.setText("To Upper Case");\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
- copy_actionPerformed(e);\r
+ copy_actionPerformed();\r
}\r
});\r
lowerCase.setText("To Lower Case");\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
public void actionPerformed(ActionEvent e)\r
{\r
- pdbFromFile_actionPerformed(e);\r
+ pdbFromFile_actionPerformed();\r
}\r
});\r
enterPDB.setText("Enter PDB Id");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- enterPDB_actionPerformed(e);\r
+ enterPDB_actionPerformed();\r
}\r
});\r
discoverPDB.setText("Discover PDB ids");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- discoverPDB_actionPerformed(e);\r
+ discoverPDB_actionPerformed();\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();\r
+ }\r
+ });\r
+ textColour.setText("Text Colour");\r
+ textColour.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ textColour_actionPerformed();\r
+ }\r
+ });\r
+ jMenu1.setText("Group");\r
add(groupMenu);\r
\r
add(sequenceMenu);\r
groupMenu.add(editMenu);\r
groupMenu.add(outputMenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(groupName);\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
- groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
- groupMenu.add(outline);\r
- sequenceMenu.add(sequenceName);\r
+ groupMenu.add(sequenceFeature);\r
+ groupMenu.add(jMenu1);\r
+ sequenceMenu.add(sequenceName);\r
sequenceMenu.add(pdbMenu);\r
+ colourMenu.add(textColour);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
pdbMenu.add(pdbFromFile);\r
pdbMenu.add(enterPDB);\r
pdbMenu.add(discoverPDB);\r
+ jMenu1.add(groupName);\r
+ jMenu1.add(unGroupMenuItem);\r
+ jMenu1.add(colourMenu);\r
+ jMenu1.add(showBoxes);\r
+ jMenu1.add(showText);\r
+ jMenu1.add(showColourText);\r
+ jMenu1.add(outline);\r
noColourmenuItem.setText("None");\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- noColourmenuItem_actionPerformed(e);\r
+ noColourmenuItem_actionPerformed();\r
}\r
});\r
\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- clustalColour_actionPerformed(e);\r
+ clustalColour_actionPerformed();\r
}\r
});\r
zappoColour.setText("Zappo");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- zappoColour_actionPerformed(e);\r
+ zappoColour_actionPerformed();\r
}\r
});\r
taylorColour.setText("Taylor");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- taylorColour_actionPerformed(e);\r
+ taylorColour_actionPerformed();\r
}\r
});\r
hydrophobicityColour.setText("Hydrophobicity");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- hydrophobicityColour_actionPerformed(e);\r
+ hydrophobicityColour_actionPerformed();\r
}\r
});\r
helixColour.setText("Helix propensity");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- helixColour_actionPerformed(e);\r
+ helixColour_actionPerformed();\r
}\r
});\r
strandColour.setText("Strand propensity");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- strandColour_actionPerformed(e);\r
+ strandColour_actionPerformed();\r
}\r
});\r
turnColour.setText("Turn propensity");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- turnColour_actionPerformed(e);\r
+ turnColour_actionPerformed();\r
}\r
});\r
buriedColour.setText("Buried Index");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- buriedColour_actionPerformed(e);\r
+ buriedColour_actionPerformed();\r
}\r
});\r
abovePIDColour.setText("Above % Identity");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- abovePIDColour_actionPerformed(e);\r
+ abovePIDColour_actionPerformed();\r
}\r
});\r
userDefinedColour.setText("User Defined...");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- PIDColour_actionPerformed(e);\r
+ PIDColour_actionPerformed();\r
}\r
});\r
BLOSUM62Colour.setText("BLOSUM62");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- BLOSUM62Colour_actionPerformed(e);\r
+ BLOSUM62Colour_actionPerformed();\r
}\r
});\r
conservationMenuItem.setText("Conservation");\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- conservationMenuItem_actionPerformed(e);\r
+ conservationMenuItem_actionPerformed();\r
}\r
});\r
}\r
if (ap.overviewPanel != null)\r
ap.overviewPanel.updateOverviewImage();\r
\r
- ap.seqPanel.repaint();\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());\r
}\r
\r
/**\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
+ protected void clustalColour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.getSequences(true),\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
ap.av.alignment.getWidth());\r
refresh();\r
}\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
+ protected void zappoColour_actionPerformed()\r
{\r
getGroup().cs = new ZappoColourScheme();\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
+ protected void taylorColour_actionPerformed()\r
{\r
getGroup().cs = new TaylorColourScheme();\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ protected void hydrophobicityColour_actionPerformed()\r
{\r
getGroup().cs = new HydrophobicColourScheme();\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
+ protected void helixColour_actionPerformed()\r
{\r
getGroup().cs = new HelixColourScheme();\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
+ protected void strandColour_actionPerformed()\r
{\r
getGroup().cs = new StrandColourScheme();\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
+ protected void turnColour_actionPerformed()\r
{\r
getGroup().cs = new TurnColourScheme();\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
+ protected void buriedColour_actionPerformed()\r
{\r
getGroup().cs = new BuriedColourScheme();\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
+ public void nucleotideMenuItem_actionPerformed()\r
{\r
getGroup().cs = new NucleotideColourScheme();\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void abovePIDColour_actionPerformed(ActionEvent e)\r
+ protected void abovePIDColour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
if(sg.cs==null)\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(ap.av.hiddenRepSequences), 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
* @param e DOCUMENT ME!\r
*/\r
- protected void PIDColour_actionPerformed(ActionEvent e)\r
+ protected void PIDColour_actionPerformed()\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(ap.av.hiddenRepSequences),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
refresh();\r
}\r
\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ protected void BLOSUM62Colour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\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(ap.av.hiddenRepSequences),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1));\r
\r
refresh();\r
}\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ protected void noColourmenuItem_actionPerformed()\r
{\r
getGroup().cs = null;\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
if(sg.cs==null)\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.getSequences(true), 0,\r
- ap.av.alignment.getWidth());\r
+ sg.getSequences(ap.av.hiddenRepSequences),\r
+ sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
\r
c.calculate();\r
c.verdict(false, ap.av.ConsPercGaps);\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void groupName_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
- String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
- "Enter new group name", "Edit group name",\r
- JOptionPane.QUESTION_MESSAGE);\r
-\r
- if (reply == null)\r
- {\r
- return;\r
- }\r
-\r
- sg.setName(reply);\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
+ protected void groupName_actionPerformed()\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
+ SequenceGroup sg = getGroup();\r
+ EditNameDialog dialog = new EditNameDialog(sg.getName(),\r
+ sg.getDescription(),\r
+ " Group Name ",\r
+ "Group Description ",\r
+ "Edit Group Name/Description");\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
+ if (!dialog.accept)\r
+ {\r
+ return;\r
+ }\r
\r
- sb.append("Something amazing will happen soon");\r
- cap.setText(sb.toString());\r
+ sg.setName(dialog.getName());\r
+ sg.setDescription(dialog.getDescription());\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- void sequenceName_actionPerformed(ActionEvent e)\r
+ void sequenceName_actionPerformed()\r
{\r
- JLabel idlabel = new JLabel( " Sequence Name ");\r
- JLabel desclabel = new JLabel("Sequence Description ");\r
- idlabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
- desclabel.setFont(new Font("Courier", Font.PLAIN, 12));\r
- JTextField id = new JTextField(sequence.getName(), 40);\r
- JTextField description = new JTextField(sequence.getDescription(), 40);\r
- JPanel panel = new JPanel(new BorderLayout());\r
- JPanel panel2 = new JPanel(new BorderLayout());\r
- panel2.add(idlabel, BorderLayout.WEST);\r
- panel2.add(id, BorderLayout.CENTER);\r
- panel.add(panel2, BorderLayout.NORTH);\r
- panel2 = new JPanel(new BorderLayout());\r
- panel2.add(desclabel, BorderLayout.WEST);\r
- panel2.add(description, BorderLayout.CENTER);\r
- panel.add(panel2, BorderLayout.SOUTH);\r
-\r
-\r
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- panel, "Edit Sequence Name/Description",\r
- JOptionPane.OK_CANCEL_OPTION );\r
-\r
-\r
- if (reply != JOptionPane.OK_OPTION )\r
+ EditNameDialog dialog = new EditNameDialog(sequence.getName(),\r
+ sequence.getDescription(),\r
+ " Sequence Name ",\r
+ "Sequence Description ",\r
+ "Edit Sequence Name/Description");\r
+\r
+ if (!dialog.accept)\r
{\r
return;\r
}\r
\r
- String s = id.getText();\r
-\r
- if (s != null)\r
+ if (dialog.getName() != null)\r
{\r
- if (s.indexOf(" ") > -1)\r
+ if (dialog.getName().indexOf(" ") > -1)\r
{\r
JOptionPane.showMessageDialog(ap,\r
"Spaces have been converted to \"_\"",\r
JOptionPane.WARNING_MESSAGE);\r
}\r
\r
- s = s.replace(' ', '_');\r
- sequence.getDatasetSequence().setName(s);\r
- sequence.setName(s);\r
+ sequence.setName(dialog.getName().replace(' ', '_'));\r
ap.repaint();\r
}\r
\r
- sequence.getDatasetSequence().setDescription(description.getText());\r
- sequence.setDescription(description.getText());\r
+ sequence.setDescription(dialog.getDescription());\r
+\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
}\r
\r
/**\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- void unGroupMenuItem_actionPerformed(ActionEvent e)\r
+ void unGroupMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
ap.av.alignment.deleteGroup(sg);\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void outline_actionPerformed(ActionEvent e)\r
+ protected void outline_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- public void showBoxes_actionPerformed(ActionEvent e)\r
+ public void showBoxes_actionPerformed()\r
{\r
getGroup().setDisplayBoxes(showBoxes.isSelected());\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- public void showText_actionPerformed(ActionEvent e)\r
+ public void showText_actionPerformed()\r
{\r
getGroup().setDisplayText(showText.isSelected());\r
refresh();\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- public void showColourText_actionPerformed(ActionEvent e)\r
+ public void showColourText_actionPerformed()\r
{\r
getGroup().setColourText(showColourText.isSelected());\r
refresh();\r
void hideSequences(boolean representGroup)\r
{\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null || sg.getSize(false)<1)\r
+ if(sg==null || sg.getSize()<1)\r
{\r
- ap.av.hideSequence(sequence);\r
+ ap.av.hideSequence(new SequenceI[]{sequence});\r
return;\r
}\r
\r
- int index = 0;\r
- while(index < sg.getSize(false))\r
- {\r
- if(representGroup && sg.getSequenceAt(index)!=sequence)\r
- {\r
- sequence.addHiddenSequence(sg.getSequenceAt(index));\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
- }\r
- else if(!representGroup)\r
- {\r
- ap.av.hideSequence(sg.getSequenceAt(index));\r
- }\r
- index ++;\r
- }\r
+ ap.av.setSelectionGroup(null);\r
\r
- ap.av.setSelectionGroup(null);\r
+ if (representGroup)\r
+ {\r
+ ap.av.hideRepSequences(sequence, sg);\r
+\r
+ return;\r
+ }\r
+\r
+ int gsize = sg.getSize();\r
+ SequenceI[] hseqs;\r
+\r
+ hseqs = new SequenceI[gsize];\r
+\r
+ int index = 0;\r
+ for (int i = 0; i < gsize; i++)\r
+ {\r
+ hseqs[index++] = sg.getSequenceAt(i);\r
+ }\r
+\r
+ ap.av.hideSequence(hseqs);\r
}\r
\r
- public void copy_actionPerformed(ActionEvent e)\r
+ public void copy_actionPerformed()\r
{\r
ap.alignFrame.copy_actionPerformed(null);\r
}\r
\r
- public void cut_actionPerformed(ActionEvent e)\r
+ public void cut_actionPerformed()\r
{\r
ap.alignFrame.cut_actionPerformed(null);\r
}\r
\r
- public void upperCase_actionPerformed(ActionEvent e)\r
+ void changeCase(ActionEvent e)\r
{\r
+ Object source = e.getSource();\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null)\r
- return;\r
-\r
- for(int g=0; g<sg.getSize(true); g++)\r
+ Vector regions = new Vector();\r
+ if (sg != null)\r
{\r
- ( (SequenceI)sg.getSequences(true).elementAt(g))\r
- .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);\r
- }\r
- ap.repaint();\r
- }\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
\r
- public void lowerCase_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg==null)\r
- return;\r
+ do\r
+ {\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
- for(int g=0; g<sg.getSize(true); g++)\r
- {\r
- ( (SequenceI)sg.getSequences(true).elementAt(g))\r
- .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);\r
- }\r
- ap.repaint();\r
- }\r
+ regions.addElement(new int[]\r
+ {start, end});\r
\r
- public void toggle_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- if (sg == null)\r
- return;\r
+ if (ap.av.hasHiddenColumns)\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
- for (int g = 0; g < sg.getSize(true); g++)\r
- {\r
- ( (SequenceI)sg.getSequences(true).elementAt(g))\r
- .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);\r
- }\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
- ap.repaint();\r
+\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
+\r
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
+ description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),\r
+ 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
}\r
\r
\r
- public void pdbFromFile_actionPerformed(ActionEvent e)\r
+ public void pdbFromFile_actionPerformed()\r
{\r
jalview.io.JalviewFileChooser chooser\r
= new jalview.io.JalviewFileChooser(jalview.bin.Cache.\r
\r
}\r
\r
- public void enterPDB_actionPerformed(ActionEvent e)\r
+ public void enterPDB_actionPerformed()\r
{\r
String id = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
"Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);\r
}\r
}\r
\r
- public void discoverPDB_actionPerformed(ActionEvent e)\r
+ public void discoverPDB_actionPerformed()\r
{\r
new jalview.io.DBRefFetcher(\r
ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);\r
}\r
+\r
+ public void sequenceFeature_actionPerformed()\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg==null)\r
+ return;\r
+\r
+ int gSize= sg.getSize();\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
+ public void textColour_actionPerformed()\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ if (sg != null)\r
+ new TextColourChooser().chooseColour(ap, sg);\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff