+/*\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
+\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.schemes.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
+import java.util.Vector;\r
\r
-public class APopupMenu extends java.awt.PopupMenu\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+\r
+public class APopupMenu\r
+ extends java.awt.PopupMenu\r
{\r
Menu groupMenu = new Menu();\r
- Menu analyze = new Menu();\r
- Menu defineMenu = new Menu();\r
- Menu groupName = new Menu();\r
- Menu groupAnnotation = new Menu();\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
- Menu residueMenu = new Menu();\r
- MenuItem annotateResidue = new MenuItem();\r
-\r
- Sequence sequence;\r
+ final AlignmentPanel ap;\r
MenuItem unGroupMenuItem = new MenuItem();\r
- MenuItem outline = 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
+ 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
\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
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if (sg != null)\r
+ {\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
+ {\r
+ groupMenu.remove(unGroupMenuItem);\r
+ }\r
+\r
+ if (seq != null && 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
+ String id = seq.getName();\r
+ if(id.indexOf("|")>-1)\r
+ id = id.substring(id.lastIndexOf("|")+1);\r
+\r
+ final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
+ + id +\r
+ link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\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
+ add(linkMenu);\r
\r
+ item = new MenuItem("Show PDB Structure");\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addPDB(seq);\r
+ }\r
+ });\r
\r
- if(seq!=null)\r
- residueMenu.setEnabled(false);\r
- else\r
- sequenceMenu.setEnabled(false);\r
+ add(item);\r
\r
+\r
+ }\r
+ }\r
+\r
+ void addPDB(Sequence seq)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame.applet);\r
+ cap.setText("Paste your PDB file here.");\r
+ cap.setPDBImport(seq, ap.seqPanel.seqCanvas);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);\r
}\r
- private void jbInit() throws Exception\r
+\r
+ private void jbInit()\r
+ throws Exception\r
{\r
groupMenu.setLabel("Group");\r
- analyze.setLabel("Analyze");\r
- analyze.addActionListener(new java.awt.event.ActionListener()\r
+ groupMenu.setLabel("Define");\r
+\r
+ unGroupMenuItem.setLabel("Remove Group");\r
+ unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- analyze_actionPerformed(e);\r
+ unGroupMenuItem_actionPerformed(e);\r
}\r
});\r
- defineMenu.setLabel("Define");\r
- groupName.setLabel("Name");\r
- groupName.addActionListener(new java.awt.event.ActionListener()\r
+\r
+ nucleotideMenuItem.setLabel("Nucleotide");\r
+ nucleotideMenuItem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupName_actionPerformed(e);\r
+ nucleotideMenuItem_actionPerformed(e);\r
}\r
});\r
- groupAnnotation.setEnabled(false);\r
- groupAnnotation.setLabel("Annotation");\r
- groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
+ conservationMenuItem.addItemListener(new ItemListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void itemStateChanged(ItemEvent itemEvent)\r
{\r
- groupAnnotation_actionPerformed(e);\r
+ conservationMenuItem_itemStateChanged(itemEvent);\r
}\r
});\r
- sequenceMenu.setLabel("Sequence");\r
- sequenceName.setLabel("Edit name");\r
- sequenceName.addActionListener(new java.awt.event.ActionListener()\r
+ abovePIDColour.addItemListener(new ItemListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void itemStateChanged(ItemEvent itemEvent)\r
{\r
- sequenceName_actionPerformed(e);\r
+ abovePIDColour_itemStateChanged(itemEvent);\r
}\r
});\r
- residueMenu.setLabel("Residue");\r
- annotateResidue.setEnabled(false);\r
- annotateResidue.setActionCommand("annotate residue");\r
- annotateResidue.setLabel("annotate residue???");\r
- unGroupMenuItem.setLabel("Remove Group");\r
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ colourMenu.setLabel("Group Colour");\r
+ showBoxes.setLabel("Boxes");\r
+ showBoxes.setState(true);\r
+ showBoxes.addItemListener(new ItemListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void itemStateChanged(ItemEvent itemEvent)\r
{\r
- unGroupMenuItem_actionPerformed(e);\r
+ showBoxes_itemStateChanged(itemEvent);\r
}\r
});\r
\r
- outline.setLabel("Border colour");\r
- outline.addActionListener(new java.awt.event.ActionListener()\r
+ showText.setLabel("Text");\r
+ showText.addItemListener(new ItemListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void itemStateChanged(ItemEvent itemEvent)\r
{\r
- outline_actionPerformed(e);\r
+ showText_itemStateChanged(itemEvent);\r
}\r
});\r
- nucleotideMenuItem.setLabel("Nucleotide");\r
- nucleotideMenuItem.addActionListener(new ActionListener()\r
+ showColourText.setLabel("Colour Text");\r
+ showColourText.addItemListener(new ItemListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void itemStateChanged(ItemEvent itemEvent)\r
{\r
- nucleotideMenuItem_actionPerformed(e);\r
+ showColourText_itemStateChanged(itemEvent);\r
}\r
});\r
\r
add(groupMenu);\r
- this.add(sequenceMenu);\r
- this.add(residueMenu);\r
- groupMenu.add(defineMenu);\r
groupMenu.add(unGroupMenuItem);\r
+ groupMenu.add(colourMenu);\r
groupMenu.addSeparator();\r
- groupMenu.add(analyze);\r
- defineMenu.add(groupName);\r
- defineMenu.add(groupAnnotation);\r
- defineMenu.addSeparator();\r
- defineMenu.add(outline);\r
- defineMenu.addSeparator();\r
- defineMenu.add(noColourmenuItem);\r
- defineMenu.add(clustalColour);\r
- defineMenu.add(BLOSUM62Colour);\r
- defineMenu.add(PIDColour);\r
-\r
- defineMenu.add(zappoColour);\r
- defineMenu.add(taylorColour);\r
- defineMenu.add(hydrophobicityColour);\r
- defineMenu.add(helixColour);\r
- defineMenu.add(strandColour);\r
- defineMenu.add(turnColour);\r
- defineMenu.add(buriedColour);\r
- defineMenu.add(nucleotideMenuItem);\r
-\r
- defineMenu.add(userDefinedColour);\r
-\r
- defineMenu.addSeparator();\r
- defineMenu.add(abovePIDColour);\r
- defineMenu.add(conservationMenuItem);\r
-\r
- sequenceMenu.add(sequenceName);\r
- residueMenu.add(annotateResidue);\r
+ groupMenu.add(showBoxes);\r
+ groupMenu.add(showText);\r
+ groupMenu.add(showColourText);\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideMenuItem);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(abovePIDColour);\r
+ colourMenu.add(conservationMenuItem);\r
\r
noColourmenuItem.setLabel("None");\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
}\r
});\r
abovePIDColour.setLabel("Above % Identity");\r
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- abovePIDColour_actionPerformed(e);\r
- }\r
- });\r
+\r
userDefinedColour.setLabel("User Defined");\r
userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
}\r
});\r
conservationMenuItem.setLabel("Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
-\r
\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
+ if(sg!=null)\r
+ {\r
+ SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
\r
- ap.seqPanel.repaint();\r
+ if (superG != null)\r
+ {\r
+ superG.setSuperGroupProperties(sg);\r
+ }\r
+ }\r
+ ap.seqPanel.seqCanvas.repaint();\r
+ if(ap.overviewPanel!=null)\r
+ ap.overviewPanel.updateOverviewImage();\r
}\r
\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
refresh();\r
}\r
\r
-\r
protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
getGroup().cs = new HydrophobicColourScheme();\r
refresh();\r
}\r
\r
-\r
-\r
- protected void abovePIDColour_actionPerformed(ActionEvent e)\r
+ protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
{\r
SequenceGroup sg = getGroup();\r
+ if(sg.cs==null)\r
+ return;\r
+\r
if (abovePIDColour.getState())\r
{\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 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
{\r
- UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());\r
+ new UserDefinedColours(ap, getGroup());\r
}\r
\r
protected void PIDColour_actionPerformed(ActionEvent e)\r
{\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
+ refresh();\r
}\r
\r
protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
sg.cs = new Blosum62ColourScheme();\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ ap.av.alignment.getWidth()));\r
\r
refresh();\r
}\r
\r
-\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
getGroup().cs = null;\r
refresh();\r
}\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
{\r
SequenceGroup sg = getGroup();\r
+ if(sg.cs==null)\r
+ return;\r
\r
- if(conservationMenuItem.getState())\r
+ if (conservationMenuItem.getState())\r
{\r
\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
- ap.av.alignment.getWidth());\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ ap.av.alignment.getWidth());\r
\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+ c.calculate();\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
\r
+ sg.cs.setConservation(c);\r
\r
- sg.cs = ccs;\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
- protected void groupAnnotation_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void groupName_actionPerformed(ActionEvent e)\r
- {\r
- /* SequenceGroup sg = getGroup();\r
- String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
- if(reply==null)\r
- return;\r
-\r
- sg.setName(reply);\r
- groupName.setLabel(reply);*/\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
- }\r
-\r
SequenceGroup getGroup()\r
{\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
+ ap.av.alignment.addGroup(sg);\r
\r
return sg;\r
}\r
\r
- void sequenceName_actionPerformed(ActionEvent e)\r
+ void unGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
- /* String id = sequence.getName();\r
- String s = (String)JOptionPane.showInternalInputDialog(\r
- ap,\r
- "Edit sequence name",\r
- "Edit sequence name ("+sequence.getName()+")",\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- null,\r
- id);\r
-\r
- if(s!=null)\r
- {\r
- sequence.setName(s);\r
- ap.repaint();\r
- }*/\r
-\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ap.av.alignment.deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ ap.repaint();\r
}\r
\r
- void unGroupMenuItem_actionPerformed(ActionEvent e)\r
+ public void showColourText_itemStateChanged(ItemEvent itemEvent)\r
{\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
+ getGroup().setColourText(showColourText.getState());\r
+ refresh();\r
}\r
\r
+ public void showText_itemStateChanged(ItemEvent itemEvent)\r
+ {\r
+ getGroup().setDisplayText(showText.getState());\r
+ refresh();\r
+ }\r
\r
- protected void outline_actionPerformed(ActionEvent e)\r
+ public void showBoxes_itemStateChanged(ItemEvent itemEvent)\r
{\r
- /* SequenceGroup sg = getGroup();\r
- Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);\r
- if(col!=null)\r
- sg.setOutlineColour(col);*/\r
+ getGroup().setDisplayBoxes(showBoxes.getState());\r
+ refresh();\r
}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff