/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.schemes.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-public class APopupMenu extends java.awt.PopupMenu\r
+import jalview.analysis.*;\r
+import jalview.commands.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+\r
+public class APopupMenu\r
+ extends java.awt.PopupMenu implements ActionListener, ItemListener\r
{\r
Menu groupMenu = new Menu();\r
+ MenuItem editGroupName = new MenuItem();\r
protected MenuItem clustalColour = new MenuItem();\r
protected MenuItem zappoColour = new MenuItem();\r
protected MenuItem taylorColour = new MenuItem();\r
MenuItem noColourmenuItem = new MenuItem();\r
protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
\r
-\r
- AlignmentPanel ap;\r
- Menu sequenceMenu = new Menu();\r
- MenuItem sequenceName = new MenuItem();\r
- Sequence sequence;\r
+ final AlignmentPanel ap;\r
MenuItem unGroupMenuItem = new MenuItem();\r
MenuItem nucleotideMenuItem = new MenuItem();\r
Menu colourMenu = new Menu();\r
CheckboxMenuItem showBoxes = new CheckboxMenuItem();\r
CheckboxMenuItem showText = new CheckboxMenuItem();\r
CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
-\r
- public APopupMenu(AlignmentPanel ap, Sequence seq)\r
+ Menu editMenu = new Menu("Edit");\r
+ MenuItem copy = new MenuItem("Copy (Jalview Only)");\r
+ MenuItem cut = new MenuItem("Cut (Jalview Only)");\r
+ MenuItem toUpper = new MenuItem("To Upper Case");\r
+ MenuItem toLower = new MenuItem("To Lower Case");\r
+ MenuItem toggleCase = new MenuItem("Toggle Case");\r
+ Menu outputmenu = new Menu();\r
+ Menu seqMenu = new Menu();\r
+ MenuItem pdb = new MenuItem();\r
+ MenuItem hideSeqs = new MenuItem();\r
+ MenuItem repGroup = new MenuItem();\r
+ MenuItem sequenceName = new MenuItem("Edit Name/Description");\r
+\r
+ Sequence seq;\r
+ MenuItem revealAll = new MenuItem();\r
+ Menu menu1 = new Menu();\r
+\r
+ public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
{\r
///////////////////////////////////////////////////////////\r
// If this is activated from the sequence panel, the user may want to\r
// If from the IDPanel, we must display the sequence menu\r
//////////////////////////////////////////////////////////\r
\r
- this.ap = ap;\r
- sequence = seq;\r
+ this.ap = apanel;\r
+ this.seq = seq;\r
\r
try\r
- { jbInit(); }\r
- catch(Exception e)\r
- { e.printStackTrace(); }\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;\r
+ i++)\r
+ {\r
+ MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter.\r
+ WRITEABLE_FORMATS[i]);\r
+\r
+ item.addActionListener(this);\r
+ outputmenu.add(item);\r
+ }\r
\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg!=null)\r
+\r
+ if (sg != null && sg.getSize() > 0)\r
{\r
+ editGroupName.setLabel(sg.getName());\r
showText.setState(sg.getDisplayText());\r
showColourText.setState(sg.getColourText());\r
showBoxes.setState(sg.getDisplayBoxes());\r
- }\r
-\r
- if( !ap.av.alignment.getGroups().contains(sg))\r
+ if (!ap.av.alignment.getGroups().contains(sg))\r
+ {\r
groupMenu.remove(unGroupMenuItem);\r
+ }\r
\r
- if(seq==null)\r
- remove(sequenceMenu);\r
+ }\r
+ else\r
+ {\r
+ remove(hideSeqs);\r
+ remove(groupMenu);\r
+ }\r
\r
+ if (links != null)\r
+ {\r
+ Menu linkMenu = new Menu("Link");\r
+ MenuItem item;\r
+ String link;\r
+ for (int i = 0; i < links.size(); i++)\r
+ {\r
+ link = links.elementAt(i).toString();\r
+ final String target = link.substring(0, link.indexOf("|"));\r
+ item = new MenuItem(target);\r
+\r
+ final String url;\r
+\r
+ if (link.indexOf("$SEQUENCE_ID$") > -1)\r
+ {\r
+ String id = seq.getName();\r
+ if (id.indexOf("|") > -1)\r
+ {\r
+ id = id.substring(id.lastIndexOf("|") + 1);\r
+ }\r
+\r
+ url = link.substring(link.indexOf("|") + 1,\r
+ link.indexOf("$SEQUENCE_ID$"))\r
+ + id +\r
+ link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+ }\r
+ else\r
+ {\r
+ url = link.substring(link.lastIndexOf("|") + 1);\r
+ }\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.showURL(url, target);\r
+ }\r
+ });\r
+ linkMenu.add(item);\r
+ }\r
+ if (seq != null)\r
+ {\r
+ seqMenu.add(linkMenu);\r
+ }\r
+ else\r
+ {\r
+ add(linkMenu);\r
+ }\r
+ }\r
+ if (seq != null)\r
+ {\r
+ seqMenu.setLabel(seq.getName());\r
+ repGroup.setLabel("Represent Group with " + seq.getName());\r
+ }\r
+ else\r
+ {\r
+ remove(seqMenu);\r
+ }\r
\r
+ if (!ap.av.hasHiddenRows)\r
+ {\r
+ remove(revealAll);\r
+ }\r
}\r
- private void jbInit() throws Exception\r
+\r
+ public void itemStateChanged(ItemEvent evt)\r
{\r
- groupMenu.setLabel("Group");\r
- groupMenu.setLabel("Define");\r
+ if (evt.getSource() == abovePIDColour)\r
+ {\r
+ abovePIDColour_itemStateChanged();\r
+ }\r
+ else if (evt.getSource() == showColourText)\r
+ {\r
+ showColourText_itemStateChanged();\r
+ }\r
+ else if (evt.getSource() == showText)\r
+ {\r
+ showText_itemStateChanged();\r
+ }\r
+ else if (evt.getSource() == showBoxes)\r
+ {\r
+ showBoxes_itemStateChanged();\r
+ }\r
+ }\r
\r
- sequenceMenu.setLabel("Sequence");\r
- sequenceName.setLabel("Edit name");\r
- unGroupMenuItem.setLabel("Remove Group");\r
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ Object source = evt.getSource();\r
+ if (source == clustalColour)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- unGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
+ clustalColour_actionPerformed();\r
+ }\r
+ else if (source == zappoColour)\r
+ {\r
+ zappoColour_actionPerformed();\r
+ }\r
+ else if (source == taylorColour)\r
+ {\r
+ taylorColour_actionPerformed();\r
+ }\r
+ else if (source == hydrophobicityColour)\r
+ {\r
+ hydrophobicityColour_actionPerformed();\r
+ }\r
+ else if (source == helixColour)\r
+ {\r
+ helixColour_actionPerformed();\r
+ }\r
+ else if (source == strandColour)\r
+ {\r
+ strandColour_actionPerformed();\r
+ }\r
+ else if (source == turnColour)\r
+ {\r
+ turnColour_actionPerformed();\r
+ }\r
+ else if (source == buriedColour)\r
+ {\r
+ buriedColour_actionPerformed();\r
+ }\r
+ else if (source == nucleotideMenuItem)\r
+ {\r
+ nucleotideMenuItem_actionPerformed();\r
+ }\r
\r
+ else if (source == userDefinedColour)\r
+ {\r
+ userDefinedColour_actionPerformed();\r
+ }\r
+ else if (source == PIDColour)\r
+ {\r
+ PIDColour_actionPerformed();\r
+ }\r
+ else if (source == BLOSUM62Colour)\r
+ {\r
+ BLOSUM62Colour_actionPerformed();\r
+ }\r
+ else if (source == noColourmenuItem)\r
+ {\r
+ noColourmenuItem_actionPerformed();\r
+ }\r
+ else if (source == conservationMenuItem)\r
+ {\r
+ conservationMenuItem_itemStateChanged();\r
+ }\r
+ else if (source == unGroupMenuItem)\r
+ {\r
+ unGroupMenuItem_actionPerformed();\r
+ }\r
\r
- nucleotideMenuItem.setLabel("Nucleotide");\r
- nucleotideMenuItem.addActionListener(new ActionListener()\r
+ else if (source == sequenceName)\r
{\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- nucleotideMenuItem_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.addItemListener(new ItemListener()\r
+ editName();\r
+ }\r
+ else if (source == pdb)\r
+ {\r
+ addPDB();\r
+ }\r
+ else if (source == hideSeqs)\r
+ {\r
+ hideSequences(false);\r
+ }\r
+ else if (source == repGroup)\r
{\r
- public void itemStateChanged(ItemEvent itemEvent)\r
+ hideSequences(true);\r
+ }\r
+ else if (source == revealAll)\r
+ {\r
+ ap.av.showAllHiddenSeqs();\r
+ }\r
+\r
+ else if (source == editGroupName)\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ getGroup().getName(),\r
+ getGroup().getDescription(),\r
+ " Group Name",\r
+ "Group Description",\r
+ ap,\r
+ "Edit Group Name / Description");\r
+\r
+ if (dialog.accept)\r
{\r
- conservationMenuItem_itemStateChanged(itemEvent);\r
+\r
+ getGroup().setName(dialog.getName().replace(' ', '_'));\r
+ getGroup().setDescription(dialog.getDescription());\r
}\r
- });\r
- abovePIDColour.addItemListener(new ItemListener()\r
+\r
+ }\r
+ else if (source == copy)\r
+ {\r
+ ap.alignFrame.copy_actionPerformed();\r
+ }\r
+ else if (source == cut)\r
{\r
- public void itemStateChanged(ItemEvent itemEvent)\r
+ ap.alignFrame.cut_actionPerformed();\r
+ }\r
+ else if (source == toUpper || source == toLower || source == toggleCase)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ Vector regions = new Vector();\r
+ if (sg != null)\r
{\r
- abovePIDColour_itemStateChanged(itemEvent);\r
+ int start = sg.getStartRes();\r
+ int end = sg.getEndRes() + 1;\r
+\r
+ do\r
+ {\r
+ if (ap.av.hasHiddenColumns)\r
+ {\r
+ if (start == 0)\r
+ {\r
+ start = ap.av.colSel.adjustForHiddenColumns(start);\r
+ }\r
+\r
+ end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+ if (start == end)\r
+ {\r
+ end = sg.getEndRes() + 1;\r
+ }\r
+ if (end > sg.getEndRes())\r
+ {\r
+ end = sg.getEndRes() + 1;\r
+ }\r
+ }\r
+\r
+ regions.addElement(new int[]\r
+ {start, end});\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
+ while (end < sg.getEndRes());\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
+ String description;\r
+ int caseChange;\r
+\r
+ if (source == toggleCase)\r
+ {\r
+ description = "Toggle Case";\r
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
+ }\r
+ else if (source == toUpper)\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
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+\r
}\r
- });\r
+ }\r
+ else\r
+ {\r
+ outputText(evt);\r
+ }\r
+\r
+ }\r
+\r
+ void outputText(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
+\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Selection output - " + e.getActionCommand(),\r
+ 600, 500);\r
+\r
+ cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(\r
+ e.getActionCommand(),\r
+ new Alignment(ap.av.getSelectionAsNewSequence()),\r
+ ap.av.showJVSuffix));\r
+\r
+ }\r
+\r
+ void editName()\r
+ {\r
+ EditNameDialog dialog = new EditNameDialog(\r
+ seq.getName(),\r
+ seq.getDescription(),\r
+ " Sequence Name",\r
+ "Sequence Description",\r
+ ap,\r
+ "Edit Sequence Name / Description");\r
+\r
+ if (dialog.accept)\r
+ {\r
+ seq.setName(dialog.getName());\r
+ seq.setDescription(dialog.getDescription());\r
+ ap.paintAlignment(false);\r
+ }\r
+ }\r
+\r
+ void addPDB()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
+ cap.setText("Paste your PDB file here.");\r
+ cap.setPDBImport(seq);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ groupMenu.setLabel("Group");\r
+ groupMenu.setLabel("Selection");\r
+\r
+ editGroupName.addActionListener(this);\r
+ unGroupMenuItem.setLabel("Remove Group");\r
+ unGroupMenuItem.addActionListener(this);\r
+\r
+ nucleotideMenuItem.setLabel("Nucleotide");\r
+ nucleotideMenuItem.addActionListener(this);\r
+ conservationMenuItem.addItemListener(this);\r
+ abovePIDColour.addItemListener(this);\r
colourMenu.setLabel("Group Colour");\r
showBoxes.setLabel("Boxes");\r
showBoxes.setState(true);\r
- showBoxes.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent itemEvent)\r
- {\r
- showBoxes_itemStateChanged(itemEvent);\r
- }\r
- });\r
+ showBoxes.addItemListener(this);\r
+ sequenceName.addActionListener(this);\r
\r
showText.setLabel("Text");\r
- showText.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent itemEvent)\r
- {\r
- showText_itemStateChanged(itemEvent);\r
- }\r
- });\r
+ showText.addItemListener(this);\r
showColourText.setLabel("Colour Text");\r
- showColourText.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent itemEvent)\r
- {\r
- showColourText_itemStateChanged(itemEvent);\r
- }\r
- });\r
-\r
+ showColourText.addItemListener(this);\r
+ outputmenu.setLabel("Output to Textbox...");\r
+ seqMenu.setLabel("Sequence");\r
+ pdb.setLabel("View PDB Structure");\r
+ hideSeqs.setLabel("Hide Sequences");\r
+ repGroup.setLabel("Represent Group with");\r
+ revealAll.setLabel("Reveal All");\r
+ menu1.setLabel("Group");\r
add(groupMenu);\r
- this.add(sequenceMenu);\r
- groupMenu.add(unGroupMenuItem);\r
- groupMenu.add(colourMenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(showBoxes);\r
- groupMenu.add(showText);\r
- groupMenu.add(showColourText);\r
- sequenceMenu.add(sequenceName);\r
+ this.add(seqMenu);\r
+ this.add(hideSeqs);\r
+ this.add(revealAll);\r
+ groupMenu.add(editGroupName);\r
+ groupMenu.add(editMenu);\r
+ groupMenu.add(outputmenu);\r
+ groupMenu.add(menu1);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
colourMenu.add(conservationMenuItem);\r
\r
noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
+ noColourmenuItem.addActionListener(this);\r
\r
clustalColour.setLabel("Clustalx colours");\r
- clustalColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
+ clustalColour.addActionListener(this);\r
zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
+ zappoColour.addActionListener(this);\r
taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
+ taylorColour.addActionListener(this);\r
hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
+ hydrophobicityColour.addActionListener(this);\r
helixColour.setLabel("Helix propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
+ helixColour.addActionListener(this);\r
strandColour.setLabel("Strand propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
+ strandColour.addActionListener(this);\r
turnColour.setLabel("Turn propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
+ turnColour.addActionListener(this);\r
buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
+ buriedColour.addActionListener(this);\r
abovePIDColour.setLabel("Above % Identity");\r
\r
userDefinedColour.setLabel("User Defined");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
+ userDefinedColour.addActionListener(this);\r
PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
+ PIDColour.addActionListener(this);\r
BLOSUM62Colour.setLabel("BLOSUM62");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
+ BLOSUM62Colour.addActionListener(this);\r
conservationMenuItem.setLabel("Conservation");\r
\r
-\r
+ editMenu.add(copy);\r
+ copy.addActionListener(this);\r
+ editMenu.add(cut);\r
+ cut.addActionListener(this);\r
+ editMenu.add(toUpper);\r
+ toUpper.addActionListener(this);\r
+ editMenu.add(toLower);\r
+ toLower.addActionListener(this);\r
+ editMenu.add(toggleCase);\r
+ seqMenu.add(sequenceName);\r
+ seqMenu.add(pdb);\r
+ seqMenu.add(repGroup);\r
+ menu1.add(unGroupMenuItem);\r
+ menu1.add(colourMenu);\r
+ menu1.add(showBoxes);\r
+ menu1.add(showText);\r
+ menu1.add(showColourText);\r
+ toggleCase.addActionListener(this);\r
+ pdb.addActionListener(this);\r
+ hideSeqs.addActionListener(this);\r
+ repGroup.addActionListener(this);\r
+ revealAll.addActionListener(this);\r
}\r
\r
void refresh()\r
{\r
- SequenceGroup sg = getGroup();\r
- SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
- if( superG !=null)\r
- superG.setSuperGroupProperties( sg );\r
-\r
- ap.seqPanel.seqCanvas.repaint();\r
+ ap.paintAlignment(true);\r
}\r
\r
- protected void clustalColour_actionPerformed(ActionEvent e)\r
+ protected void clustalColour_actionPerformed()\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
+ sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),\r
+ ap.av.alignment.getWidth());\r
refresh();\r
}\r
\r
- protected void zappoColour_actionPerformed(ActionEvent e)\r
+ protected void zappoColour_actionPerformed()\r
{\r
getGroup().cs = new ZappoColourScheme();\r
refresh();\r
}\r
\r
- protected void taylorColour_actionPerformed(ActionEvent e)\r
+ protected void taylorColour_actionPerformed()\r
{\r
getGroup().cs = new TaylorColourScheme();\r
refresh();\r
}\r
\r
-\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
+ protected void hydrophobicityColour_actionPerformed()\r
{\r
getGroup().cs = new HydrophobicColourScheme();\r
refresh();\r
}\r
\r
- protected void helixColour_actionPerformed(ActionEvent e)\r
+ protected void helixColour_actionPerformed()\r
{\r
getGroup().cs = new HelixColourScheme();\r
refresh();\r
}\r
\r
- protected void strandColour_actionPerformed(ActionEvent e)\r
+ protected void strandColour_actionPerformed()\r
{\r
getGroup().cs = new StrandColourScheme();\r
refresh();\r
}\r
\r
- protected void turnColour_actionPerformed(ActionEvent e)\r
+ protected void turnColour_actionPerformed()\r
{\r
getGroup().cs = new TurnColourScheme();\r
refresh();\r
}\r
\r
- protected void buriedColour_actionPerformed(ActionEvent e)\r
+ protected void buriedColour_actionPerformed()\r
{\r
getGroup().cs = new BuriedColourScheme();\r
refresh();\r
}\r
\r
- public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
+ public void nucleotideMenuItem_actionPerformed()\r
{\r
getGroup().cs = new NucleotideColourScheme();\r
refresh();\r
}\r
\r
-\r
-\r
- protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
+ protected void abovePIDColour_itemStateChanged()\r
{\r
SequenceGroup sg = getGroup();\r
+ if (sg.cs == null)\r
+ {\r
+ return;\r
+ }\r
+\r
if (abovePIDColour.getState())\r
{\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
+ hiddenRepSequences), 0,\r
ap.av.alignment.getWidth()));\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
- if (sg.cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
+ getGroup().getName());\r
\r
- SliderPanel.showPIDSlider();\r
+ sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
\r
+ SliderPanel.showPIDSlider();\r
\r
}\r
else // remove PIDColouring\r
{\r
- ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
- rcs.setThreshold(0);\r
- sg.cs = rcs;\r
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
}\r
\r
refresh();\r
\r
}\r
\r
-\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
+ protected void userDefinedColour_actionPerformed()\r
{\r
- new UserDefinedColours( ap, getGroup());\r
+ new UserDefinedColours(ap, getGroup());\r
}\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.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
+ hiddenRepSequences), 0,\r
+ ap.av.alignment.getWidth()));\r
refresh();\r
}\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.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.\r
+ hiddenRepSequences), 0,\r
+ ap.av.alignment.getWidth()));\r
\r
refresh();\r
}\r
\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ protected void noColourmenuItem_actionPerformed()\r
{\r
getGroup().cs = null;\r
refresh();\r
}\r
\r
- protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
+ protected void conservationMenuItem_itemStateChanged()\r
{\r
SequenceGroup sg = getGroup();\r
-\r
- if(conservationMenuItem.getState())\r
+ if (sg.cs == null)\r
{\r
+ return;\r
+ }\r
\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
- ap.av.alignment.getWidth());\r
+ if (conservationMenuItem.getState())\r
+ {\r
\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.getSequences(ap.av.\r
+ hiddenRepSequences), 0,\r
+ ap.av.alignment.getWidth());\r
\r
+ c.calculate();\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
\r
- sg.cs = ccs;\r
+ sg.cs.setConservation(c);\r
\r
- SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
SliderPanel.showConservationSlider();\r
}\r
else // remove ConservationColouring\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
+ sg.cs.setConservation(null);\r
}\r
\r
- refresh();\r
- }\r
-\r
-\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for(int i=0; i<sg.sequences.size(); i++)\r
- {\r
- Sequence tmp = (Sequence)sg.sequences.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
+ refresh();\r
}\r
\r
SequenceGroup getGroup()\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
// this method won't add a new group if it already exists\r
- ap.av.alignment.addGroup(sg);\r
+ if (sg != null)\r
+ {\r
+ ap.av.alignment.addGroup(sg);\r
+ }\r
\r
return sg;\r
}\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
- ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ap.av.alignment.deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ ap.paintAlignment(true);\r
}\r
\r
-\r
- public void showColourText_itemStateChanged(ItemEvent itemEvent)\r
+ public void showColourText_itemStateChanged()\r
{\r
getGroup().setColourText(showColourText.getState());\r
refresh();\r
}\r
\r
- public void showText_itemStateChanged(ItemEvent itemEvent)\r
+ public void showText_itemStateChanged()\r
{\r
getGroup().setDisplayText(showText.getState());\r
refresh();\r
}\r
\r
- public void showBoxes_itemStateChanged(ItemEvent itemEvent)\r
+ public void showBoxes_itemStateChanged()\r
{\r
getGroup().setDisplayBoxes(showBoxes.getState());\r
refresh();\r
}\r
\r
+ void hideSequences(boolean representGroup)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg == null || sg.getSize() < 1)\r
+ {\r
+ ap.av.hideSequence(new SequenceI[]\r
+ {seq});\r
+ return;\r
+ }\r
+\r
+ ap.av.setSelectionGroup(null);\r
+\r
+ if (representGroup)\r
+ {\r
+ ap.av.hideRepSequences(seq, 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
}\r
git://source.jalview.org / jalview.git / blobdiff