protected Vector groups = new Vector();\r
protected ArrayList superGroup = new ArrayList();\r
protected char gapCharacter = '-';\r
+ public AlignmentAnnotation [] annotations;\r
+ public Conservation conservation;\r
+\r
public boolean featuresAdded = false;\r
\r
/** Make an alignment from an array of Sequences.\r
return false;\r
\r
return true;\r
+ }\r
+\r
+ public void deleteAnnotation(AlignmentAnnotation aa)\r
+ {\r
+ int aSize = 1;\r
+ if(annotations!=null)\r
+ aSize = annotations.length;\r
+\r
+ AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize-1];\r
+\r
+ int tIndex = 0;\r
+ for (int i = 0; i < aSize; i++)\r
+ {\r
+ if(annotations[i]==aa)\r
+ continue;\r
+\r
+\r
+ temp[tIndex] = annotations[i];\r
+ tIndex++;\r
+ }\r
+\r
+ annotations = temp;\r
\r
+ }\r
+\r
+ public void addAnnotation(AlignmentAnnotation aa)\r
+ {\r
+ int aSize = 1;\r
+ if(annotations!=null)\r
+ aSize = annotations.length+1;\r
+\r
+ AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize];\r
+ int i=0;\r
+ if (aSize > 1)\r
+ for (i = 0; i < aSize-1; i++)\r
+ temp[i] = annotations[i];\r
+\r
+ temp[i] = aa;\r
+\r
+ annotations = temp;\r
}\r
+ public AlignmentAnnotation[] getAlignmentAnnotation()\r
+ {\r
+ return annotations;\r
+ }\r
+\r
}\r
\r
\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+public class AlignmentAnnotation\r
+{\r
+ public String label;\r
+ public String description;\r
+ public Annotation [] annotations;\r
+ public boolean isGraph = false;\r
+ public float graphMin, graphMax;\r
+ public int windowLength;\r
+\r
+ // Graphical hints and tips\r
+ public boolean editable = false;\r
+ public boolean hasIcons; //\r
+ public boolean hasText;\r
+ public boolean visible = true;\r
+ public int height=0;\r
+\r
+ public AlignmentAnnotation(String label, String description, Annotation [] annotations)\r
+ {\r
+ // always editable?\r
+ editable = true;\r
+ this.label = label;\r
+ this.description = description;\r
+ this.annotations = annotations;\r
+ for(int i=0; i<annotations.length; i++)\r
+ {\r
+ if (annotations[i]!=null &&(\r
+ annotations[i].secondaryStructure == 'H' ||\r
+ annotations[i].secondaryStructure == 'E'))\r
+ hasIcons = true;\r
+\r
+ if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)\r
+ hasText = true;\r
+ }\r
+ }\r
+\r
+ public AlignmentAnnotation(String label, String description, Annotation [] annotations, float min, float max, int winLength)\r
+ {\r
+ // graphs are not editable\r
+ this.label = label;\r
+ this.description = description;\r
+ this.annotations = annotations;\r
+ isGraph = true;\r
+ graphMin = min;\r
+ graphMax = max;\r
+ windowLength = winLength;\r
+ for(int i=0; i<annotations.length; i++)\r
+ {\r
+ if (annotations[i]!=null &&(\r
+ annotations[i].secondaryStructure == 'H' ||\r
+ annotations[i].secondaryStructure == 'E'))\r
+ hasIcons = true;\r
+\r
+ if (annotations[i]!=null && annotations[i].displayCharacter.length()>0)\r
+ hasText = true;\r
+ }\r
+\r
+\r
+ }\r
+\r
+}\r
package jalview.datamodel;\r
\r
-import jalview.jbgui.*;\r
import java.util.*;\r
\r
/** Data structure to hold and manipulate a multiple sequence alignment\r
public void sortByPID(SequenceI s) ;\r
public void sortByID() ;\r
\r
+ //Annotations\r
+ public void addAnnotation(AlignmentAnnotation aa);\r
+ public void deleteAnnotation(AlignmentAnnotation aa);\r
+ public AlignmentAnnotation [] getAlignmentAnnotation();\r
+\r
public void setGapCharacter(char gc);\r
public char getGapCharacter();\r
\r
- public Vector getAAFrequency();\r
+ public Vector getAAFrequency();\r
}\r
\r
\r
--- /dev/null
+package jalview.datamodel;
+import java.awt.*;
+
+public class Annotation
+{
+ public String displayCharacter="";
+ public String description=""; // currently used as mouse over
+ public char secondaryStructure=' '; // recognises H and E
+ public float value;
+
+ // add visual cues here
+ public Color colour = Color.black;
+
+ public Annotation(String displayChar, String desc, char ss, float val)
+ {
+ displayCharacter = displayChar;
+ description = desc;
+ secondaryStructure = ss;
+ value = val;
+ }
+}
final AlignViewport viewport;\r
public AlignFrame(AlignmentI al)\r
{\r
- super();\r
viewport = new AlignViewport(al,true,true,false);\r
\r
String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
alignPanel = new AlignmentPanel(this, viewport);\r
getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
\r
+ // add conservation graph to alignment\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
+\r
+ alignPanel.annotationPanel.adjustPanelHeight();\r
+ alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+ alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+\r
+\r
addInternalFrameListener(new InternalFrameAdapter()\r
{\r
public void internalFrameActivated(InternalFrameEvent evt)\r
seq = (SequenceI[]) history[1];\r
viewport.setAlignment( new Alignment(seq) );\r
updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.RefreshPanels();\r
alignPanel.RefreshPanels();\r
}\r
\r
int newHeight = newSeqs.length * af.viewport.getCharHeight() + 200;\r
if (newHeight > 500)\r
newHeight = 500;\r
- Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
+ Desktop.addInternalFrame(af, "Copied sequences", 700, 500);\r
}\r
else\r
{\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
}\r
\r
{\r
this.setClosed(true);\r
}catch(Exception ex){}\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
\r
}\r
SequenceI[] seq = (SequenceI[]) history[1];\r
viewport.setAlignment( new Alignment(seq) );\r
updateEditMenuBar();\r
+ viewport.updateConsensus();\r
+ alignPanel.RefreshPanels();\r
alignPanel.RefreshPanels();\r
}\r
\r
{\r
addHistoryItem("delete gapped columns");\r
viewport.getAlignment().removeGaps();\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
}\r
\r
jSize--;\r
}\r
}\r
-\r
+ viewport.updateConservation();\r
+ viewport.updateConsensus();\r
alignPanel.RefreshPanels();\r
}\r
\r
alignPanel.RefreshPanels();\r
}\r
\r
- public void consensusGraphMenuItem_actionPerformed(ActionEvent e)\r
+ public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
- alignPanel.setGraphPanelVisible( consensusGraphMenuItem.isSelected() );\r
+ alignPanel.setAnnotationVisible( annotationPanelMenuItem.isSelected() );\r
}\r
\r
public void overviewMenuItem_actionPerformed(ActionEvent e)\r
g.drawString("Clustal Alignment Web Service running", 30,30);\r
}\r
}\r
- public void jpredMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- // JInternalFrame frame = new JInternalFrame();\r
-// JPredClient ct = new JPredClient((SequenceI)\r
- /// viewport.getAlignment().getSequences().elementAt(0));\r
+ protected void jpred_actionPerformed(ActionEvent e)\r
+{\r
+\r
+\r
+ JInternalFrame frame = new JInternalFrame();\r
+ JPredClient ct = new JPredClient((SequenceI)\r
+ viewport.getAlignment().getSequences().elementAt(0));\r
}\r
\r
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
package jalview.gui;\r
\r
import java.awt.*;\r
-import jalview.io.*;\r
+import jalview.analysis.*;\r
import jalview.analysis.NJTree;\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
\r
ColumnSelection colSel = new ColumnSelection();\r
\r
- String visibleConsensus;\r
\r
int threshold;\r
int increment;\r
NJTree currentTree = null;\r
\r
\r
- public AlignViewport(AlignmentI da,\r
+ public AlignViewport(AlignmentI al,\r
boolean showText,\r
boolean showBoxes,\r
boolean wrapAlignment) {\r
- this(0,da.getWidth()-1,0,da.getHeight()-1,\r
- showText,\r
- showBoxes,\r
- wrapAlignment);\r
-\r
- setAlignment(da);\r
- }\r
\r
- public AlignViewport(int startRes, int endRes,\r
- int startSeq, int endSeq,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\r
-\r
- this.startRes = startRes;\r
- this.endRes = endRes;\r
- this.startSeq = startSeq;\r
- this.endSeq = endSeq;\r
- this.showText = showText;\r
- this.showBoxes = showBoxes;\r
+ this.startRes = 0;\r
+ this.endRes = al.getWidth()-1;\r
+ this.startSeq = 0;\r
+ this.endSeq = al.getHeight()-1;\r
+ this.showText = showText;\r
+ this.showBoxes = showBoxes;\r
this.wrapAlignment = wrapAlignment;\r
\r
+ setAlignment(al);\r
setFont( font );\r
}\r
\r
showSequenceFeatures = b;\r
}\r
\r
+ AlignmentAnnotation consensus;\r
+ AlignmentAnnotation conservation;\r
+ public void updateConservation()\r
+ {\r
+ Annotation [] annotations = new Annotation[alignment.getWidth()];\r
+\r
+ Conservation cons = new jalview.analysis.Conservation("All",\r
+ jalview.schemes.ResidueProperties.propHash, 3,\r
+ alignment.getSequences(), 0,\r
+ alignment.getWidth());\r
+ cons.calculate();\r
+ cons.verdict(false, 100);\r
+\r
+ String sequence = cons.getConsSequence().getSequence();\r
+ for (int i = 0; i < alignment.getWidth(); i++)\r
+ {\r
+ int value = 0;\r
+ try\r
+ {\r
+ value = Integer.parseInt(sequence.charAt(i) + "");\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ if (sequence.charAt(i) == '*') value = 10;\r
+ }\r
+\r
+ annotations[i] = new Annotation(sequence.charAt(i) + "",\r
+ "Conservation graph", ' ', value);\r
+ }\r
+\r
+ if(conservation==null)\r
+ {\r
+ conservation = new AlignmentAnnotation("Conservation",\r
+ "Conservation of total alignment",\r
+ annotations, 0, 10, 1);\r
+ alignment.addAnnotation(conservation);\r
+ }\r
+ else\r
+ conservation.annotations = annotations;\r
+\r
+ }\r
+\r
+ public void updateConsensus()\r
+ {\r
+ Annotation [] annotations = new Annotation[alignment.getWidth()];\r
+\r
+ Vector cons = alignment.getAAFrequency();\r
+ Hashtable hash = null;\r
+ for (int i = 0; i < alignment.getWidth(); i++)\r
+ {\r
+ hash = (Hashtable) cons.elementAt(i);\r
+ float value = Float.parseFloat(hash.get("maxCount").toString());\r
+ value /= Float.parseFloat(hash.get("size").toString());\r
+\r
+ value *= 100;\r
+ String maxRes = hash.get("maxResidue")+" ";\r
+ String mouseOver = hash.get("maxResidue")+" ";\r
+ if(maxRes.length()>2)\r
+ {\r
+ mouseOver = "["+maxRes+"] ";\r
+ maxRes = "+ ";\r
+ }\r
+\r
+ mouseOver += value+"%";\r
+ annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+\r
+ }\r
+\r
+ if(consensus==null)\r
+ {\r
+ consensus = new AlignmentAnnotation("% Identity",\r
+ "PID", annotations, 0f, 100f, 1);\r
+ alignment.addAnnotation(consensus);\r
+ }\r
+ else\r
+ consensus.annotations = annotations;\r
+\r
+ }\r
+\r
public String getVisibleConsensus()\r
{\r
return visibleConsensus;\r
}\r
\r
- Vector consensus = new Vector();\r
+ String visibleConsensus;\r
+ Vector consensusV = new Vector();\r
public Vector getConsensus(boolean recalculate)\r
{\r
- if(recalculate || consensus.size()<1)\r
+ if(recalculate || consensusV.size()<1)\r
{\r
- consensus = alignment.getAAFrequency();\r
+ consensusV = alignment.getAAFrequency();\r
StringBuffer sb = new StringBuffer();\r
Hashtable hash = null;\r
- for (int i = 0; i < consensus.size(); i++)\r
+ for (int i = 0; i < consensusV.size(); i++)\r
{\r
- hash = (Hashtable) consensus.elementAt(i);\r
+ hash = (Hashtable) consensusV.elementAt(i);\r
sb.append(hash.get("maxResidue").toString().charAt(0));\r
}\r
visibleConsensus = sb.toString();\r
}\r
\r
\r
- return consensus;\r
+ return consensusV;\r
}\r
\r
+\r
public SequenceGroup getSelectionGroup()\r
{\r
return selectionGroup;\r
SeqPanel seqPanel;\r
IdPanel idPanel;\r
IdwidthAdjuster idwidthAdjuster;\r
- SecondaryStructurePanel ssPanel;\r
public AlignFrame alignFrame;\r
ScalePanel scalePanel;\r
- ScorePanel scorePanel;\r
+ AnnotationPanel annotationPanel;\r
+ AnnotationLabels alabels;\r
\r
public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
{\r
idPanel = new IdPanel (av, this);\r
\r
scalePanel = new ScalePanel(av, this);\r
- scorePanel = new ScorePanel(av);\r
- ssPanel = new SecondaryStructurePanel(av);\r
-\r
- secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);\r
\r
idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
idwidthAdjuster = new IdwidthAdjuster(this);\r
idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
\r
+ annotationPanel = new AnnotationPanel(this);\r
+ alabels = new AnnotationLabels(this);\r
+\r
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());\r
+ annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
+ annotationScroller.setViewportView(annotationPanel);\r
+ annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
+\r
Dimension d = calculateIdWidth();\r
d.setSize( d.width+4, d.height);\r
idPanel.idCanvas.setPreferredSize( d );\r
hscrollFillerPanel.setPreferredSize( d );\r
\r
scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
- scorePanelHolder.add(scorePanel, BorderLayout.CENTER);\r
seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
\r
\r
Dimension d = calculateIdWidth();\r
d.setSize( d.width+4, d.height);\r
idPanel.idCanvas.setPreferredSize( d );\r
- hscrollFillerPanel.setPreferredSize( d );\r
RefreshPanels();\r
}\r
});\r
RefreshPanels();\r
break;\r
case KeyEvent.VK_X:\r
+ if(evt.isControlDown())\r
alignFrame.cut_actionPerformed(null);\r
break;\r
case KeyEvent.VK_C:\r
+ if(evt.isControlDown())\r
alignFrame.copy_actionPerformed(null);\r
break;\r
case KeyEvent.VK_V:\r
+ if(evt.isControlDown())\r
alignFrame.paste(true);\r
break;\r
case KeyEvent.VK_A:\r
+ if(evt.isControlDown())\r
alignFrame.selectAllSequenceMenuItem_actionPerformed(null);\r
break;\r
case KeyEvent.VK_DOWN:\r
alignFrame.moveSelectedSequences(true);\r
break;\r
case KeyEvent.VK_F:\r
+ if(evt.isControlDown())\r
alignFrame.findMenuItem_actionPerformed(null);\r
break;\r
}\r
}\r
\r
\r
- public void setGraphPanelVisible(boolean b)\r
+ public void setAnnotationVisible(boolean b)\r
{\r
- idSpaceFillerPanel.setVisible(b);\r
- scorePanelHolder.setVisible(b);\r
+ annotationSpaceFillerHolder.setVisible(b);\r
+ annotationScroller.setVisible(b);\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ RefreshPanels();\r
+ }\r
+ });\r
\r
- RefreshPanels();\r
- // bit annoying to call this twice, can you do better?\r
- RefreshPanels();\r
}\r
\r
- public void setSecondaryStructureVisible(boolean b)\r
- {\r
- secondaryPanelHolder.setVisible(b);\r
- RefreshPanels();\r
- }\r
\r
public void setWrapAlignment(boolean wrap)\r
{\r
- scorePanelHolder.setVisible(!wrap);\r
scalePanelHolder.setVisible(!wrap);\r
- secondaryPanelHolder.setVisible(!wrap);\r
-\r
hscroll.setVisible(!wrap);\r
-\r
idwidthAdjuster.setVisible(!wrap);\r
- idSpaceFillerPanel.setVisible(!wrap);\r
+ annotationScroller.setVisible(!wrap);\r
+ annotationSpaceFillerHolder.setVisible(!wrap);\r
idSpaceFillerPanel1.setVisible(!wrap);\r
\r
RefreshPanels();\r
RefreshPanels();\r
}\r
\r
+\r
public void RefreshPanels()\r
{\r
+ requestFocus();\r
+ invalidate();\r
+\r
+ Dimension d = idPanel.idCanvas.getPreferredSize();\r
+ idPanelHolder.setPreferredSize(d);\r
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));\r
\r
- requestFocus();\r
- invalidate();\r
- idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());\r
- if(idPanel.idCanvas.getPreferredSize()!=null)\r
- hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.getPreferredSize().width, 12));\r
- idSpaceFillerPanel1.setPreferredSize(new Dimension(500,\r
- av.charHeight / 2 + 12));\r
- scalePanelHolder.setPreferredSize(new Dimension(500,\r
- av.charHeight / 2 + 12));\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- int max = av.alignment.getWidth() /\r
- (seqPanel.seqCanvas.getWidth() / av.charWidth)+1 ;\r
-\r
- vscroll.setValues(0, 1, 0, max);\r
- }\r
- else\r
- {\r
- av.getConsensus(true);\r
- if (overviewPanel != null)\r
- overviewPanel.updateOverviewImage();\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- }\r
-\r
- repaint();\r
+ if (av.getWrapAlignment())\r
+ {\r
+ int max = av.alignment.getWidth() /\r
+ (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;\r
+ vscroll.setValues(0, 1, 0, max);\r
+ }\r
+ else\r
+ {\r
+ if (overviewPanel != null)\r
+ overviewPanel.updateOverviewImage();\r
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ }\r
+\r
+ validate();\r
+ repaint();\r
}\r
\r
int hextent = 0;\r
hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());\r
vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );\r
\r
- repaint();\r
-\r
}\r
\r
\r
overviewPanel.setBoxPosition();\r
\r
repaint();\r
+\r
}\r
\r
public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException\r
--- /dev/null
+\r
+package jalview.gui;\r
+\r
+import javax.swing.*;\r
+import java.awt.event.*;\r
+import java.awt.*;\r
+import java.awt.image.*;\r
+import jalview.datamodel.*;\r
+\r
+public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener\r
+{\r
+ boolean active = false;\r
+ Image image;\r
+ AlignmentPanel ap ;\r
+ boolean resizing = false;\r
+ int oldY, mouseX;\r
+ static String ADDNEW = "Add new row";\r
+ static String HIDE = "Hide this row";\r
+ static String DELETE = "Delete this row";\r
+ static String SHOWALL="Show all hidden rows";\r
+ int selectedRow = 0;\r
+ int scrollOffset = 0;\r
+\r
+ public AnnotationLabels(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+\r
+ java.net.URL url = getClass().getResource("/images/idwidth.gif");\r
+ Image temp = null;\r
+ if (url != null)\r
+ temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+\r
+ try\r
+ {\r
+ MediaTracker mt = new MediaTracker(this);\r
+ mt.addImage(temp, 0);\r
+ mt.waitForID(0);\r
+ }\r
+ catch (Exception ex) {}\r
+\r
+ BufferedImage bi = new BufferedImage(temp.getHeight(this), temp.getWidth(this),\r
+ BufferedImage.TYPE_INT_RGB);\r
+ Graphics2D g = (Graphics2D) bi.getGraphics();\r
+ g.rotate(Math.toRadians(90));\r
+ g.drawImage(temp, 0, -bi.getWidth(this), this);\r
+ image = (Image) bi;\r
+\r
+ addMouseListener(this);\r
+ addMouseMotionListener(this);\r
+ }\r
+\r
+ public void setScrollOffset(int y)\r
+ {\r
+ scrollOffset = y;\r
+ repaint();\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
+\r
+ if(evt.getActionCommand().equals(ADDNEW))\r
+ {\r
+ String label = JOptionPane.showInputDialog(this, "Label for annotation");\r
+ if(label==null)\r
+ label = "";\r
+ ap.av.alignment.addAnnotation(new AlignmentAnnotation\r
+ (label,\r
+ "New description",\r
+ new Annotation[ap.av.alignment.getWidth()]));\r
+ }\r
+ else if(evt.getActionCommand().equals(HIDE))\r
+ {\r
+ aa[selectedRow].visible = false;\r
+ }\r
+ else if(evt.getActionCommand().equals(DELETE))\r
+ {\r
+ ap.av.alignment.deleteAnnotation(aa[selectedRow]);\r
+ }\r
+ else if(evt.getActionCommand().equals(SHOWALL))\r
+ {\r
+ for(int i=0; i<aa.length; i++)\r
+ aa[i].visible = true;\r
+ }\r
+\r
+ ap.annotationPanel.adjustPanelHeight();\r
+ ap.RefreshPanels();\r
+\r
+ }\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ int y = evt.getY() - scrollOffset;\r
+\r
+ if (SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
+ if(aa==null || aa.length==0)\r
+ {\r
+ JPopupMenu pop = new JPopupMenu("Annotations");\r
+ JMenuItem item = new JMenuItem(ADDNEW);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+ return;\r
+ }\r
+\r
+ int height = 0;\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if(!aa[i].visible)\r
+ continue;\r
+\r
+ height += aa[i].height;\r
+ if(y<height)\r
+ {\r
+ selectedRow = i;\r
+ break;\r
+ }\r
+ }\r
+\r
+ JPopupMenu pop = new JPopupMenu("Annotations");\r
+ JMenuItem item = new JMenuItem(ADDNEW);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(HIDE);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(DELETE);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(SHOWALL);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+ return;\r
+ }\r
+\r
+ oldY = evt.getY();\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt){ active = false; repaint(); }\r
+ public void mouseEntered(MouseEvent evt) { active = true; repaint();}\r
+ public void mouseExited(MouseEvent evt) { active = false; repaint();}\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ active = true;\r
+ Dimension d = ap.annotationScroller.getPreferredSize();\r
+ int dif = evt.getY() - oldY;\r
+\r
+ dif /= ap.av.charHeight;\r
+ dif *= ap.av.charHeight;\r
+\r
+ if(d.height-dif>20)\r
+ {\r
+ ap.annotationScroller.setPreferredSize(new Dimension(d.width,d.height - dif));\r
+ d = ap.annotationSpaceFillerHolder.getPreferredSize();\r
+ ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,d.height - dif));\r
+ ap.RefreshPanels();\r
+ }\r
+ ap.addNotify();\r
+ }\r
+\r
+ public void mouseMoved(MouseEvent evt) {}\r
+ public void mouseClicked(MouseEvent evt) {}\r
+\r
+ public void paintComponent(Graphics g1)\r
+ {\r
+ Graphics2D g = (Graphics2D)g1;\r
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+\r
+ FontMetrics fm = g.getFontMetrics(g.getFont());\r
+\r
+ g.setColor(Color.white);\r
+ g.fillRect(0,0, getWidth(), getHeight());\r
+\r
+ g.translate(0, scrollOffset);\r
+ g.setColor(Color.black);\r
+\r
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();\r
+ int y = g.getFont().getSize();\r
+ int x = 0;\r
+\r
+ if(aa!=null)\r
+ for(int i=0; i<aa.length; i++)\r
+ {\r
+ if(!aa[i].visible)\r
+ continue;\r
+\r
+ x = getWidth() - fm.stringWidth(aa[i].label)-3;\r
+\r
+ g.drawString(aa[i].label, x, y);\r
+\r
+ y+=aa[i].height;\r
+ }\r
+\r
+ if (active)\r
+ {\r
+ if (image != null)\r
+ g.drawImage(image, 2, 0, this);\r
+ }\r
+\r
+ if (aa == null || aa.length<1)\r
+ {\r
+ g.drawString("Right click", 2, 8);\r
+ g.drawString("to add annotation", 2, 18);\r
+ }\r
+\r
+\r
+\r
+ }\r
+\r
+}\r
--- /dev/null
+package jalview.gui;\r
+\r
+import jalview.datamodel.*;\r
+\r
+import javax.swing.*;\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+import java.util.*;\r
+import java.awt.image.*;\r
+\r
+public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener\r
+{\r
+ AlignViewport av;\r
+ AlignmentPanel ap;\r
+ int activeRow =-1;\r
+\r
+ ArrayList activeRes;\r
+ static String HELIX ="Helix";\r
+ static String SHEET ="Sheet";\r
+ static String LABEL ="Label";\r
+ static String REMOVE="Remove Annotation";\r
+ static String COLOUR="Colour";\r
+ static Color HELIX_COLOUR = Color.red.darker();\r
+ static Color SHEET_COLOUR = Color.green.darker().darker();\r
+\r
+ BufferedImage bi;\r
+\r
+\r
+\r
+ public AnnotationPanel(AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ av = ap.av;\r
+ this.setLayout(null);\r
+ addMouseListener(this);\r
+ addMouseMotionListener(this);\r
+ adjustPanelHeight();\r
+\r
+\r
+ ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener( this );\r
+ }\r
+\r
+ public void adjustmentValueChanged(AdjustmentEvent evt)\r
+ {\r
+ ap.alabels.setScrollOffset( -evt.getValue() );\r
+ }\r
+\r
+ public void adjustPanelHeight()\r
+ {\r
+ // setHeight of panels\r
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+ int height = 0;\r
+ if(aa!=null)\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ if(!aa[i].visible)\r
+ continue;\r
+\r
+ aa[i].height = 0;\r
+\r
+ if(aa[i].hasText)\r
+ aa[i].height += av.charHeight;\r
+ if (aa[i].hasIcons)\r
+ aa[i].height += 16;\r
+\r
+ if (aa[i].isGraph)\r
+ aa[i].height += 50;\r
+\r
+ if(aa[i].height==0)\r
+ aa[i].height = 20;\r
+ height += aa[i].height;\r
+ }\r
+ else height=20;\r
+ this.setPreferredSize(new Dimension(1, height));\r
+\r
+ }\r
+\r
+ public void addEditableColumn(int i)\r
+ {\r
+ if(activeRow==-1)\r
+ {\r
+ AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ for(int j=0; j<aa.length; j++)\r
+ if(aa[j].editable)\r
+ {\r
+ activeRow = j;\r
+ break;\r
+ }\r
+ }\r
+\r
+ if(activeRes==null)\r
+ {\r
+ activeRes = new ArrayList();\r
+ activeRes.add(String.valueOf(i));\r
+ return;\r
+ }\r
+\r
+ activeRes.add(String.valueOf(i));\r
+\r
+ }\r
+\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+\r
+ AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ Annotation [] anot = aa[activeRow].annotations;\r
+\r
+ if(evt.getActionCommand().equals(REMOVE))\r
+ {\r
+ for(int i=0; i<activeRes.size(); i++)\r
+ {\r
+ anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
+ anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
+ }\r
+ }\r
+ else if(evt.getActionCommand().equals(LABEL))\r
+ {\r
+ String label = JOptionPane.showInputDialog(this, "Enter Label ", "Enter label", JOptionPane.QUESTION_MESSAGE );\r
+ if(label==null)\r
+ label = "";\r
+\r
+ if(label.length()>0 && !aa[activeRow].hasText)\r
+ aa[activeRow].hasText = true;\r
+\r
+ for(int i=0; i<activeRes.size(); i++)\r
+ {\r
+ int index = Integer.parseInt(activeRes.get(i).toString());\r
+ if(anot[index]==null)\r
+ anot[index] = new Annotation(label, "", ' ',0);\r
+ anot[index].displayCharacter = label;\r
+ }\r
+ }\r
+ else if(evt.getActionCommand().equals(COLOUR))\r
+ {\r
+ Color col = JColorChooser.showDialog(this, "Choose foreground colour", Color.black);\r
+ for (int i = 0; i < activeRes.size(); i++)\r
+ {\r
+ int index = Integer.parseInt(activeRes.get(i).toString());\r
+ if (anot[index] == null)\r
+ anot[index] = new Annotation("", "", ' ', 0);\r
+ anot[index].colour = col;\r
+ }\r
+ }\r
+ else // HELIX OR SHEET\r
+ {\r
+ char type = 0;\r
+ String symbol = "\u03B1";\r
+ if(evt.getActionCommand().equals(HELIX))\r
+ type = 'H';\r
+ else if(evt.getActionCommand().equals(SHEET))\r
+ {\r
+ type = 'E';\r
+ symbol = "\u03B2";\r
+ }\r
+\r
+ if(!aa[activeRow].hasIcons)\r
+ aa[activeRow].hasIcons = true;\r
+\r
+\r
+ String label = JOptionPane.showInputDialog("Enter a label for the structure?", symbol );\r
+ if(label==null)\r
+ label="";\r
+\r
+ if(label.length()>0 && !aa[activeRow].hasText)\r
+ aa[activeRow].hasText = true;\r
+\r
+ for(int i=0; i<activeRes.size(); i++)\r
+ {\r
+ int index = Integer.parseInt(activeRes.get(i).toString());\r
+ if (anot[index] == null)\r
+ {\r
+ anot[index] = new Annotation(label, "", type, 0);\r
+ }\r
+\r
+ anot[ index ].secondaryStructure = type;\r
+ anot[ index ].displayCharacter = label;\r
+ }\r
+ }\r
+\r
+ adjustPanelHeight();\r
+ activeRes = null;\r
+ repaint();\r
+ return;\r
+\r
+\r
+ }\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if (SwingUtilities.isRightMouseButton(evt))\r
+ {\r
+ if(activeRes==null)\r
+ return;\r
+\r
+ JPopupMenu pop = new JPopupMenu("Structure type");\r
+ JMenuItem item = new JMenuItem(HELIX);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(SHEET);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(LABEL);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(COLOUR);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ item = new JMenuItem(REMOVE);\r
+ item.addActionListener(this);\r
+ pop.add(item);\r
+ pop.show(this, evt.getX(), evt.getY());\r
+ return;\r
+ }\r
+\r
+\r
+ AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ if(aa==null)\r
+ return;\r
+\r
+ int height = 0;\r
+ activeRow = -1;\r
+ for(int i=0; i<aa.length; i++)\r
+ {\r
+ height+= aa[i].height;\r
+\r
+ if(evt.getY()<height)\r
+ {\r
+ if(!aa[i].editable)\r
+ {\r
+ activeRes = null;\r
+ continue;\r
+ }\r
+\r
+ activeRow = i;\r
+ break;\r
+ }\r
+ }\r
+\r
+\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+\r
+ if(evt.isControlDown() || evt.isAltDown())\r
+ addEditableColumn(res);\r
+\r
+ else if(evt.isShiftDown())\r
+ {\r
+\r
+ if(activeRes==null)\r
+ activeRes=new ArrayList();\r
+ else\r
+ {\r
+ int start = Integer.parseInt( activeRes.get( activeRes.size()-1 ).toString() );\r
+ int end = res;\r
+ if(end<start)\r
+ {\r
+ int temp = end;\r
+ end = start;\r
+ start = temp;\r
+ }\r
+ for(int n=start; n<=end; n++)\r
+ addEditableColumn(n);\r
+\r
+ }\r
+ }\r
+ else\r
+ {\r
+ activeRes = new ArrayList();\r
+ activeRes.add( String.valueOf(res) );\r
+ }\r
+\r
+ repaint();\r
+\r
+ }\r
+ public void mouseReleased(MouseEvent evt)\r
+ { }\r
+ public void mouseEntered(MouseEvent evt)\r
+ { }\r
+ public void mouseExited(MouseEvent evt)\r
+ { }\r
+ public void mouseDragged(MouseEvent evt)\r
+ { }\r
+ public void mouseMoved(MouseEvent evt)\r
+ {\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
+ AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+ if(aa==null)\r
+ return;\r
+\r
+ int row = -1;\r
+ int height=0;\r
+ for(int i=0; i<aa.length; i++)\r
+ {\r
+\r
+ if( aa[i].visible )\r
+ height += aa[i].height;\r
+\r
+ if(evt.getY()<height)\r
+ {\r
+ row = i;\r
+ break;\r
+ }\r
+ }\r
+\r
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
+ if(row>-1 && aa[row].annotations[res]!=null)\r
+ this.setToolTipText(aa[row].annotations[res].description);\r
+\r
+ }\r
+ public void mouseClicked(MouseEvent evt) {}\r
+\r
+\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ if(bi==null\r
+ || bi.getWidth()!=ap.annotationPanel.getWidth()\r
+ || bi.getHeight()!=ap.annotationPanel.getHeight())\r
+ {\r
+ bi = new BufferedImage(ap.annotationPanel.getWidth(),\r
+ ap.annotationPanel.getHeight(),\r
+ BufferedImage.TYPE_INT_RGB);\r
+ }\r
+\r
+ drawComponent( (Graphics2D)bi.getGraphics() );\r
+ g.drawImage( bi, 0, 0, this);\r
+ }\r
+\r
+ public void drawComponent(Graphics2D g)\r
+ {\r
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);\r
+ FontMetrics fm = g.getFontMetrics();\r
+ g.setFont(av.getFont());\r
+ g.setColor(Color.white);\r
+ g.fillRect(0,0,getWidth(),getHeight());\r
+\r
+ if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)\r
+ {\r
+ g.setColor(Color.black);\r
+ g.drawString("Alignment has no annotations",20,15);\r
+ return;\r
+ }\r
+\r
+ AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
+\r
+ int j, x=0, y=0;\r
+ char [] lastSS = new char[aa.length];\r
+ int [] lastSSX= new int[aa.length] ;\r
+ int iconOffset = av.charHeight/2;\r
+ boolean validRes = false;\r
+ //\u03B2 \u03B1\r
+ for(int i=0; i<aa.length; i++)\r
+ {\r
+ AlignmentAnnotation row = aa[i];\r
+ if(!row.visible)\r
+ continue;\r
+\r
+ if(row.isGraph)\r
+ {\r
+ // this is so that we draw the characters below the graph\r
+ y += row.height;\r
+ if(row.hasText)\r
+ y -= av.charHeight;\r
+ }\r
+ if(row.hasText)\r
+ iconOffset = av.charHeight/2;\r
+ else\r
+ iconOffset = 0;\r
+\r
+ for(j=av.startRes; j<av.endRes+1; j++)\r
+ {\r
+ validRes = row.annotations[j]==null?false:true;\r
+\r
+ x = (j-av.getStartRes())*av.charWidth;\r
+\r
+\r
+ if(activeRow==i)\r
+ {\r
+\r
+ g.setColor(Color.red);\r
+\r
+ if(activeRes!=null)\r
+ for (int n = 0; n < activeRes.size(); n++)\r
+ {\r
+ int v = Integer.parseInt(activeRes.get(n).toString()) ;\r
+ if (v == j)\r
+ g.fillRect( (j-av.getStartRes()) * av.charWidth, y, av.charWidth, row.height);\r
+ }\r
+ }\r
+\r
+\r
+\r
+ if(validRes && row.annotations[j].displayCharacter.length()>0)\r
+ {\r
+ int charOffset = (av.charWidth -\r
+ fm.charWidth(row.annotations[j].displayCharacter.\r
+ charAt(0))) / 2;\r
+ g.setColor( row.annotations[j].colour);\r
+ if(j==0)\r
+ {\r
+ if (row.annotations[0].secondaryStructure == 'H'\r
+ || row.annotations[0].secondaryStructure == 'E')\r
+ g.drawString(row.annotations[j].displayCharacter, x,\r
+ y + iconOffset + 2);\r
+ }\r
+ else if( (row.annotations[j].secondaryStructure=='H'\r
+ || row.annotations[j].secondaryStructure=='E') &&\r
+ (row.annotations[j-1]==null ||\r
+ row.annotations[j].secondaryStructure!=row.annotations[j-1].secondaryStructure))\r
+\r
+ g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);\r
+\r
+ if(!row.hasIcons)\r
+ g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
+ y + iconOffset + 2);\r
+ }\r
+\r
+ if(row.hasIcons)\r
+ if(!validRes || row.annotations[j].secondaryStructure!=lastSS[i])\r
+ {\r
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y+4 + iconOffset, x-lastSSX[i], 7, 8, 8);\r
+ break;\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4 + iconOffset, x-lastSSX[i]-4, 7);\r
+ g.fillPolygon(new int[] {x - 4, x- 4, x }\r
+ , new int[]{y+ iconOffset, y + 14+ iconOffset, y + 8+ iconOffset}, 3);\r
+ break;\r
+ case 'C':\r
+ break;\r
+ default :\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
+ break;\r
+ }\r
+\r
+ if(validRes)\r
+ lastSS[i] = row.annotations[j].secondaryStructure;\r
+ else\r
+ lastSS[i] = ' ';\r
+ lastSSX[i] = x;\r
+ }\r
+\r
+ if (validRes && row.isGraph)\r
+ {\r
+ g.setColor(new Color(0,0,180));\r
+ int height = (int)((row.annotations[j].value / row.graphMax)*50);\r
+\r
+ if(row.windowLength>1)\r
+ {\r
+ int total =0;\r
+ for(int i2=j- (row.windowLength/2); i2<j+(row.windowLength/2); i2++)\r
+ {\r
+ if(i2<0 || i2>=av.alignment.getWidth())\r
+ continue;\r
+\r
+ total += row.annotations[i2].value;\r
+ }\r
+\r
+ total/=row.windowLength;\r
+ height = (int)( (total / row.graphMax) *50);\r
+\r
+ }\r
+\r
+ g.fillRect(x, y-height, av.charWidth, height );\r
+ }\r
+\r
+\r
+ }\r
+\r
+ x+=av.charWidth;\r
+\r
+ if(row.hasIcons)\r
+ switch (lastSS[i])\r
+ {\r
+ case 'H':\r
+ g.setColor(HELIX_COLOUR);\r
+ g.fillRoundRect(lastSSX[i], y+4+ iconOffset, x - lastSSX[i], 7, 8, 8);\r
+ break;\r
+ case 'E':\r
+ g.setColor(SHEET_COLOUR);\r
+ g.fillRect(lastSSX[i], y + 4+ iconOffset, x - lastSSX[i] - 4, 7);\r
+ g.fillPolygon(new int[]\r
+ {x - 4, x - 4, x}\r
+ , new int[]\r
+ {y + iconOffset, y + 14+ iconOffset, y + 7+ iconOffset}\r
+ , 3);\r
+ break;\r
+ case 'C':\r
+ break;\r
+ default:\r
+ g.setColor(Color.gray);\r
+ g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
+ break;\r
+\r
+ }\r
+\r
+ if(row.isGraph && row.hasText)\r
+ y+=av.charHeight;\r
+ if(!row.isGraph)\r
+ y+=aa[i].height;\r
+ }\r
+ }\r
+\r
+ // used by overview window\r
+ public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)\r
+ {\r
+ g.setColor(Color.white);\r
+ g.fillRect(0,0,width, y);\r
+ g.setColor(new Color(0,0,180));\r
+ int x = 0;\r
+ for(int j=0; j<aa.annotations.length; j++)\r
+ {\r
+ g.setColor(new Color(0, 0, 180));\r
+ int height = (int) ( (aa.annotations[j].value / aa.graphMax) * 50);\r
+ g.fillRect(x, y - height, av.charWidth, height);\r
+ x+=av.charWidth;\r
+ }\r
+ }\r
+}\r
for (int i=0; i < size();i++) {\r
int temp = columnAt(i);\r
\r
- if (temp >= start) {\r
+ if (temp >= start)\r
selected.setElementAt(new Integer(temp-change),i);\r
- }\r
}\r
}\r
}\r
+++ /dev/null
-package jalview.gui;\r
-\r
-import jalview.jbgui.*;\r
-import java.util.*;\r
-import javax.swing.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-public class ScorePanel extends JPanel\r
-{\r
- AlignViewport av;\r
-\r
- public ScorePanel(AlignViewport a)\r
- {\r
- av = a;\r
- setPreferredSize(new Dimension(500,80));\r
- addMouseMotionListener(new MouseMotionAdapter()\r
- { public void mouseMoved(MouseEvent evt)\r
- {\r
- doMouseMoved(evt);\r
- }\r
- });\r
-\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- }\r
-\r
- public void doMouseMoved(MouseEvent evt)\r
- {\r
- Vector freq = av.getConsensus(false);\r
-\r
- int col = (int)(evt.getX()/av.charWidth) +av.getStartRes();\r
-\r
- if(col >= av.getEndRes() || col >= freq.size())\r
- return;\r
-\r
- Hashtable hash = (Hashtable) freq.elementAt( col );\r
-\r
- String characters = hash.get("maxResidue").toString();\r
-\r
- if (characters.length()>1)\r
- this.setToolTipText(characters);\r
- else\r
- this.setToolTipText(null);\r
- }\r
-\r
-\r
-\r
- public void paintComponent(Graphics g)\r
- {\r
- setPreferredSize(new Dimension( this.getWidth(), 80));\r
- drawScorePanel(g, getWidth(), av.getStartRes(), av.getChunkWidth());\r
- }\r
-\r
- public void drawScorePanel(Graphics g, int width, int startRes, int length)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0,width, 80);\r
- g.setColor(Color.blue);\r
- g.setFont(av.getFont());\r
-\r
- Vector freq = av.getConsensus(false);\r
-\r
- int value, charOffset;\r
- String characters;\r
- char character;\r
-\r
-\r
- int i=0, iSize = length;\r
- if(iSize > freq.size())\r
- iSize=freq.size();\r
-\r
- for (i = 0; i < iSize; i++)\r
- {\r
- g.setColor(Color.blue);\r
-\r
- Hashtable hash = (Hashtable) freq.elementAt(i+startRes);\r
- if(hash.containsKey("maxResidue"))\r
- characters = hash.get("maxResidue").toString();\r
- else\r
- characters="@";\r
- character = characters.charAt(0);\r
- value = Integer.parseInt(hash.get("maxCount").toString());\r
-\r
- if (characters.length() > 1)\r
- character = '+';\r
-\r
- charOffset = (int) (av.charWidth -\r
- g.getFontMetrics().charWidth(character)) / 2;\r
- g.drawString(character + "", charOffset + (int) (i * av.charWidth),\r
- 60 + (int) av.charWidth);\r
-\r
- value = (int) ( (float) value /\r
- Float.parseFloat(hash.get("size").toString()) * 55);\r
-\r
- if ( !jalview.util.Comparison.isGap(character))\r
- g.fillRect( (int) (i * av.charWidth),\r
- 60 - value,\r
- (int) av.charWidth,\r
- value\r
- );\r
- }\r
- }\r
-\r
-}\r
+++ /dev/null
-package jalview.gui;\r
-\r
-import javax.swing.JPanel;\r
-import java.awt.event.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-import javax.swing.*;\r
-import jalview.datamodel.*;\r
-\r
-public class SecondaryStructurePanel extends JPanel implements ActionListener\r
-{\r
- AlignViewport av;\r
- Vector structures;\r
-\r
- SecondaryStructure amend;\r
-\r
- public SecondaryStructurePanel(AlignViewport av)\r
- {\r
- this.av = av;\r
- structures = new Vector();\r
- setPreferredSize(new Dimension(500,30));\r
-\r
- addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- { doMousePressed(evt); }\r
- public void mouseReleased(MouseEvent evt)\r
- { doMouseReleased(evt); }\r
- });\r
- addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseDragged(MouseEvent evt)\r
- { doMouseDragged(evt); }\r
- });\r
- }\r
-\r
- int startRes = 0;\r
- int endRes = 0;\r
- boolean amendStart = false;\r
- boolean amendEnd = false;\r
-\r
- public void doMousePressed(MouseEvent evt)\r
- {\r
- amend = null;\r
- amendStart =false;\r
- amendEnd = false;\r
-\r
- startRes = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- for(int i=0; i<structures.size(); i++)\r
- {\r
- SecondaryStructure ss = (SecondaryStructure) structures.get(i);\r
- if(startRes>=ss.start && startRes<=ss.end)\r
- {\r
- amend = ss;\r
- if(startRes==ss.start)\r
- amendStart = true;\r
-\r
- if(startRes==ss.end)\r
- amendEnd = true;\r
-\r
- if(evt.getClickCount()==2)\r
- {\r
- String label = JOptionPane.showInputDialog(this, "Amend label", "Amend label", JOptionPane.QUESTION_MESSAGE );\r
- if(label==null)\r
- label = "";\r
- ss.label = label;\r
- }\r
- break;\r
- }\r
- }\r
- repaint();\r
-\r
- }\r
-\r
- public void doMouseReleased(MouseEvent evt)\r
- {\r
- endRes = evt.getX() / av.getCharWidth() + av.getStartRes();\r
-\r
- if(amend!=null)\r
- {\r
- if(amendStart)\r
- amend.start = endRes;\r
- if(amendEnd)\r
- amend.end = endRes;\r
-\r
- amend=null;\r
- repaint();\r
- return;\r
- }\r
-\r
- endRes = evt.getX() / av.getCharWidth() + av.getStartRes();\r
-\r
- JPopupMenu pop = new JPopupMenu("Structure type");\r
- JMenuItem item = new JMenuItem("Helix");\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem("Sheet");\r
- item.addActionListener(this);\r
- pop.add(item);\r
- pop.show(this, evt.getX(), evt.getY());\r
-\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
-\r
- int type = 0;\r
- if(evt.getActionCommand().equals("Helix"))\r
- type = SecondaryStructure.HELIX;\r
- else if(evt.getActionCommand().equals("Sheet"))\r
- type = SecondaryStructure.SHEET;\r
-\r
- String label = JOptionPane.showInputDialog(this, "Enter a label for the structure?", "Enter label", JOptionPane.QUESTION_MESSAGE );\r
- if(label==null)\r
- label = "";\r
-\r
- SecondaryStructure ss = new SecondaryStructure(startRes, endRes, type, label);\r
- structures.add(ss);\r
- repaint();\r
-\r
- }\r
-\r
- public void doMouseDragged(MouseEvent evt)\r
- {\r
- paintNow(getGraphics());\r
- }\r
-\r
- void paintNow(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.setFont(new Font("Verdana", Font.PLAIN, 10));\r
- g.fillRect(0,0,getWidth(),getHeight());\r
- for(int i=0; i<structures.size(); i++)\r
- {\r
- SecondaryStructure ss = (SecondaryStructure)structures.get(i);\r
-\r
-\r
- if(ss.type==SecondaryStructure.SHEET)\r
- {\r
- g.setColor(Color.orange);\r
- if(ss==amend)\r
- g.setColor(Color.red);\r
-\r
- g.fillRect( ( ss.start - av.startRes) * av.charWidth, 4,\r
- (ss.end - ss.start) * av.charWidth, 7);\r
-\r
- g.fillPolygon( new int[]{ (ss.end - av.startRes )* av.charWidth,\r
- ( ss.end - av.startRes )* av.charWidth,\r
- ( ss.end - av.startRes )* av.charWidth+7},\r
- new int[]{0,14,7}, 3);\r
- }\r
-\r
- if(ss.type==SecondaryStructure.HELIX)\r
- {\r
- g.setColor(Color.magenta);\r
- if(ss==amend)\r
- g.setColor(Color.red);\r
- g.fillRoundRect((ss.start -av.startRes)* av.charWidth, 4,\r
- (ss.end - ss.start) * av.charWidth, 7, 8,8);\r
- }\r
-\r
-\r
-\r
- g.setColor(Color.black);\r
-\r
- int labelWidth = g.getFontMetrics().stringWidth(ss.label);\r
-\r
- g.drawString( ss.label, (ss.start +(ss.end-ss.start)/2 -av.startRes)*av.charWidth - labelWidth/2, 24);\r
- }\r
- }\r
-\r
- public void paintComponent(Graphics g)\r
- {\r
- paintNow(g);\r
- }\r
-}\r
-\r
-class SecondaryStructure\r
-{\r
- public static int HELIX = 1;\r
- public static int SHEET = 2;\r
- public String label="";\r
- public int start= 20;\r
- public int end = 40;\r
- public int type = HELIX;\r
-\r
- public SecondaryStructure(int s, int e, int t, String l)\r
- {\r
- start = s; end = e; type = t; label = l;\r
- }\r
-\r
-}\r
-\r
-\r
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
JMenuItem njTreeBlosumMenuItem = new JMenuItem();
JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
- protected JCheckBoxMenuItem consensusGraphMenuItem = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
JMenuItem htmlMenuItem = new JMenuItem();
JMenuItem overviewMenuItem = new JMenuItem();
protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
JMenuItem epsFile = new JMenuItem();
JMenuItem LoadtreeMenuItem = new JMenuItem();
+ JMenuItem jpred = new JMenuItem();
public GAlignFrame()
{
njTreeBlosumMenuItem_actionPerformed(e);
}
});
- consensusGraphMenuItem.setActionCommand("");
- consensusGraphMenuItem.setText("Consensus graph");
- consensusGraphMenuItem.setState(true);
- consensusGraphMenuItem.addActionListener(new java.awt.event.ActionListener()
+ annotationPanelMenuItem.setActionCommand("");
+ annotationPanelMenuItem.setText("Annotation Panel");
+ annotationPanelMenuItem.setState(true);
+ annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- consensusGraphMenuItem_actionPerformed(e);
+ annotationPanelMenuItem_actionPerformed(e);
}
});
colourTextMenuItem.setText("Colour text");
LoadtreeMenuItem_actionPerformed(e);
}
});
+ jpred.setText("JPred");
+ jpred.addActionListener(new java.awt.event.ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ jpred_actionPerformed(e);
+ }
+ });
alignFrameMenuBar.add(fileMenu);
alignFrameMenuBar.add(editMenu);
alignFrameMenuBar.add(searchMenu);
viewMenu.add(viewTextMenuItem);
viewMenu.add(colourTextMenuItem);
viewMenu.add(renderGapsMenuItem);
- viewMenu.add(consensusGraphMenuItem);
+ viewMenu.add(annotationPanelMenuItem);
viewMenu.add(overviewMenuItem);
viewMenu.add(sequenceFeatures);
colourMenu.add(applyToAllGroups);
calculateMenu.add(avDistanceTreeBlosumMenuItem);
calculateMenu.add(njTreeBlosumMenuItem);
alignMenu.add(clustalAlignMenuItem);
+ alignMenu.add(jpred);
this.getContentPane().add(statusBar, BorderLayout.SOUTH);
jMenu1.add(pasteNew);
jMenu1.add(pasteThis);
- protected void consensusGraphMenuItem_actionPerformed(ActionEvent e)
+ protected void annotationPanelMenuItem_actionPerformed(ActionEvent e)
{
}
}
+ protected void jpred_actionPerformed(ActionEvent e)
+ {
+
+ }
+
}
import java.awt.*;
import javax.swing.*;
+import javax.swing.border.*;
public class GAlignmentPanel extends JPanel
{
protected JPanel seqPanelHolder = new JPanel();
BorderLayout borderLayout1 = new BorderLayout();
BorderLayout borderLayout3 = new BorderLayout();
- JPanel jPanel2 = new JPanel();
- BorderLayout borderLayout2 = new BorderLayout();
- protected JPanel scorePanelHolder = new JPanel();
protected JPanel scalePanelHolder = new JPanel();
protected JPanel idPanelHolder = new JPanel();
BorderLayout borderLayout5 = new BorderLayout();
protected JPanel idSpaceFillerPanel1 = new JPanel();
- protected JPanel idSpaceFillerPanel = new JPanel();
- BorderLayout borderLayout4 = new BorderLayout();
+ public JPanel annotationSpaceFillerHolder = new JPanel();
BorderLayout borderLayout6 = new BorderLayout();
ButtonGroup buttonGroup1 = new ButtonGroup();
BorderLayout borderLayout7 = new BorderLayout();
- JPanel jPanel3 = new JPanel();
- protected JPanel secondaryPanelHolder = new JPanel();
- BorderLayout borderLayout8 = new BorderLayout();
- BorderLayout borderLayout9 = new BorderLayout();
- JPanel jPanel1 = new JPanel();
+ JPanel hscrollHolder = new JPanel();
BorderLayout borderLayout10 = new BorderLayout();
protected JPanel hscrollFillerPanel = new JPanel();
BorderLayout borderLayout11 = new BorderLayout();
+ public JScrollPane annotationScroller = new JScrollPane();
+ Border border1;
+ BorderLayout borderLayout4 = new BorderLayout();
public GAlignmentPanel()
{
}
private void jbInit() throws Exception
{
+ border1 = BorderFactory.createLineBorder(Color.gray,1);
idPanelHolder.setBorder(null);
idPanelHolder.setPreferredSize(new Dimension(70, 10));
this.setLayout(borderLayout7);
sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
sequenceHolderPanel.setLayout(borderLayout3);
seqPanelHolder.setLayout(borderLayout1);
- jPanel2.setBackground(new Color(212, 208, 230));
- jPanel2.setBorder(null);
- jPanel2.setLayout(borderLayout2);
scalePanelHolder.setBackground(Color.white);
scalePanelHolder.setMinimumSize(new Dimension(10, 80));
scalePanelHolder.setPreferredSize(new Dimension(10, 30));
scalePanelHolder.setLayout(borderLayout6);
- scorePanelHolder.setBackground(Color.white);
- scorePanelHolder.setPreferredSize(new Dimension(10, 80));
- scorePanelHolder.setLayout(borderLayout4);
idPanelHolder.setLayout(borderLayout5);
idSpaceFillerPanel1.setBackground(Color.white);
idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
idSpaceFillerPanel1.setLayout(borderLayout11);
- idSpaceFillerPanel.setBackground(Color.white);
- idSpaceFillerPanel.setPreferredSize(new Dimension(10, 80));
+ annotationSpaceFillerHolder.setBackground(Color.white);
+ annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+ annotationSpaceFillerHolder.setLayout(borderLayout4);
hscroll.setOrientation(JScrollBar.HORIZONTAL);
- jPanel3.setLayout(borderLayout9);
- secondaryPanelHolder.setLayout(borderLayout8);
- jPanel1.setLayout(borderLayout10);
+ hscrollHolder.setLayout(borderLayout10);
hscrollFillerPanel.setBackground(Color.white);
- jPanel1.setBackground(Color.white);
+ hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+ hscrollHolder.setBackground(Color.white);
+ annotationScroller.setBorder(null);
+ annotationScroller.setPreferredSize(new Dimension(10, 80));
+ this.setPreferredSize(new Dimension(220, 166));
+ this.setRequestFocusEnabled(true);
sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
seqPanelHolder.add(vscroll, BorderLayout.EAST);
- this.add(jPanel2, BorderLayout.CENTER);
- jPanel2.add(sequenceHolderPanel, BorderLayout.CENTER);
- sequenceHolderPanel.add(jPanel3, BorderLayout.SOUTH);
- jPanel3.add(scorePanelHolder, BorderLayout.CENTER);
+ sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);
// jPanel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
this.add(idPanelHolder, BorderLayout.WEST);
idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
- idPanelHolder.add(idSpaceFillerPanel, BorderLayout.SOUTH);
- this.add(jPanel1, BorderLayout.SOUTH);
- jPanel1.add(hscroll, BorderLayout.CENTER);
- jPanel1.add(hscrollFillerPanel, BorderLayout.WEST);
+ idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
+ this.add(hscrollHolder, BorderLayout.SOUTH);
+ hscrollHolder.add(hscroll, BorderLayout.CENTER);
+ hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
+ this.add(sequenceHolderPanel, BorderLayout.CENTER);
}
git://source.jalview.org / jalview.git / commitdiff