MenuItem noColourmenuItem = new MenuItem();\r
protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
\r
- AlignmentPanel ap;\r
+ final AlignmentPanel ap;\r
MenuItem unGroupMenuItem = new MenuItem();\r
MenuItem nucleotideMenuItem = new MenuItem();\r
Menu colourMenu = new Menu();\r
CheckboxMenuItem showText = new CheckboxMenuItem();\r
CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
\r
- public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)\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
+ this.ap = apanel;\r
\r
try\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
- + seq.getName() +\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
- jalview.bin.JalviewLite.showURL(url, target);\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
+ 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
+\r
private void jbInit()\r
throws Exception\r
{\r
refresh();\r
}\r
\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\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
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.GAlignFrame;\r
import jalview.schemes.*;\r
import jalview.datamodel.*;\r
import jalview.analysis.*;\r
import java.util.*;\r
import java.io.InputStreamReader;\r
import java.io.BufferedReader;\r
+import java.net.URL;\r
\r
-public class AlignFrame\r
- extends GAlignFrame\r
+\r
+public class AlignFrame extends Frame\r
{\r
final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
+ public final AlignViewport viewport;\r
int NEW_WINDOW_WIDTH = 700;\r
int NEW_WINDOW_HEIGHT = 500;\r
jalview.bin.JalviewLite applet;\r
\r
public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)\r
{\r
+ try{\r
+ jbInit();\r
+ }catch(Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
this.applet = applet;\r
viewport = new AlignViewport(al, applet);\r
alignPanel = new AlignmentPanel(this, viewport);\r
\r
}\r
\r
+ public AlignViewport getAlignViewport()\r
+ {\r
+ return viewport;\r
+ }\r
+\r
+ public SeqCanvas getSeqcanvas()\r
+ {\r
+ return alignPanel.seqPanel.seqCanvas;\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+\r
+ public void parseFeaturesFile(String file)\r
+ {\r
+ try\r
+ {\r
+ URL url = new URL(file);\r
+\r
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));\r
+ SequenceI seq = null;\r
+ String line, type, desc, token;\r
+\r
+ int index, start, end;\r
+ StringTokenizer st;\r
+ SequenceFeature sf;\r
+ FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ int lineNo = 0;\r
+ while ( (line = in.readLine()) != null)\r
+ {\r
+ lineNo++;\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() == 2)\r
+ {\r
+ type = st.nextToken();\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ continue;\r
+ }\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ desc = st.nextToken();\r
+ token = st.nextToken();\r
+ if (!token.equals("ID_NOT_SPECIFIED"))\r
+ {\r
+ index = viewport.alignment.findIndex(viewport.alignment.findName(\r
+ token));\r
+ st.nextToken();\r
+ }\r
+ else\r
+ {\r
+ index = Integer.parseInt(st.nextToken());\r
+ }\r
+\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+\r
+ seq = viewport.alignment.getSequenceAt(index);\r
+ start = seq.findIndex(start) - 1;\r
+ end = seq.findIndex(end) - 1;\r
+\r
+ type = st.nextToken();\r
+\r
+ if(fr.getColour(type)==null)\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ }\r
+\r
+ sf = new SequenceFeature(type, desc, "", start, end);\r
+\r
+ seq.addSequenceFeature(sf);\r
+ }\r
+ }\r
+\r
+ viewport.showSequenceFeatures = true;\r
+\r
+ alignPanel.repaint();\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Error parsing groups file: " + ex);\r
+ }\r
+ }\r
+\r
+\r
public void inputText_actionPerformed(ActionEvent e)\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
jalview.bin.JalviewLite.addFrame(frame,\r
"Alignment output - " + e.getActionCommand(),\r
600, 500);\r
- cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),\r
- viewport.getAlignment().\r
- getSequences()));\r
+ cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment().getSequences(),\r
+ viewport.showJVSuffix));\r
}\r
\r
public void closeMenuItem_actionPerformed(ActionEvent e)\r
{\r
PaintRefresher.components.remove(viewport.alignment);\r
- dispose();\r
if(PaintRefresher.components.size()==0 && applet==null)\r
System.exit(0);\r
}\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
alignPanel.repaint();\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
new FontChooser(alignPanel);\r
}\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+\r
+ public void seqLimits_itemStateChanged(ItemEvent e)\r
{\r
- viewport.setShowFullId(fullSeqId.getState());\r
+ viewport.setShowJVSuffix(seqLimits.getState());\r
alignPanel.fontChanged();\r
alignPanel.repaint();\r
}\r
\r
+\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setColourText(colourTextMenuItem.getState());\r
\r
protected void documentation_actionPerformed(ActionEvent e)\r
{\r
- jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
+ showURL("http://www.jalview.org/help.html");\r
}\r
\r
protected void about_actionPerformed(ActionEvent e)\r
jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
\r
}\r
+\r
+ /**\r
+ * Displays the given URL in a new browser window\r
+ *\r
+ * @param url URL to display in browser window.\r
+ * <br>New window will be named "HELP_WINDOW"\r
+ */\r
+ public void showURL(String url)\r
+ {\r
+ showURL(url, "HELP");\r
+ }\r
+\r
+ public void showURL(String url, String target)\r
+ {\r
+ if (applet == null)\r
+ {\r
+ System.out.println("Not running as applet - no browser available.");\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ applet.getAppletContext().showDocument(new java.net.URL(url),\r
+ target);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ //////////////////////////////////////////////////////////////////////////////////\r
+ //JBuilder Graphics here\r
+\r
+ protected MenuBar alignFrameMenuBar = new MenuBar();\r
+ protected Menu fileMenu = new Menu();\r
+ protected MenuItem closeMenuItem = new MenuItem();\r
+ protected Menu editMenu = new Menu();\r
+ protected Menu viewMenu = new Menu();\r
+ protected Menu colourMenu = new Menu();\r
+ protected Menu calculateMenu = new Menu();\r
+ protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
+ protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
+ protected MenuItem invertSequenceMenuItem = new MenuItem();\r
+ protected MenuItem remove2LeftMenuItem = new MenuItem();\r
+ protected MenuItem remove2RightMenuItem = new MenuItem();\r
+ protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+ protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+ protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
+ protected MenuItem sortIDMenuItem = new MenuItem();\r
+ protected MenuItem sortGroupMenuItem = new MenuItem();\r
+ protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
+ protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+ protected MenuItem PCAMenuItem = new MenuItem();\r
+ protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+ protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ public Label statusBar = new Label();\r
+ protected Menu outputTextboxMenu = new Menu();\r
+ protected MenuItem clustalColour = new MenuItem();\r
+ protected MenuItem zappoColour = new MenuItem();\r
+ protected MenuItem taylorColour = new MenuItem();\r
+ protected MenuItem hydrophobicityColour = new MenuItem();\r
+ protected MenuItem helixColour = new MenuItem();\r
+ protected MenuItem strandColour = new MenuItem();\r
+ protected MenuItem turnColour = new MenuItem();\r
+ protected MenuItem buriedColour = new MenuItem();\r
+ protected MenuItem userDefinedColour = new MenuItem();\r
+ protected MenuItem PIDColour = new MenuItem();\r
+ protected MenuItem BLOSUM62Colour = new MenuItem();\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+ protected MenuItem undoMenuItem = new MenuItem();\r
+ protected MenuItem redoMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+ protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+ MenuItem findMenuItem = new MenuItem();\r
+ Menu searchMenu = new Menu();\r
+ protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+ protected MenuItem nucleotideColour = new MenuItem();\r
+ MenuItem deleteGroups = new MenuItem();\r
+ MenuItem delete = new MenuItem();\r
+ MenuItem copy = new MenuItem();\r
+ MenuItem cut = new MenuItem();\r
+ Menu Menu1 = new Menu();\r
+ MenuItem pasteNew = new MenuItem();\r
+ MenuItem pasteThis = new MenuItem();\r
+ protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+ protected MenuItem font = new MenuItem();\r
+ protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+ MenuItem modifyPID = new MenuItem();\r
+ MenuItem modifyConservation = new MenuItem();\r
+ protected Menu sortByTreeMenu = new Menu();\r
+ Menu sort = new Menu();\r
+ Menu calculate = new Menu();\r
+ MenuItem inputText = new MenuItem();\r
+ Menu helpMenu = new Menu();\r
+ MenuItem documentation = new MenuItem();\r
+ MenuItem about = new MenuItem();\r
+ protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+\r
+ private void jbInit() throws Exception {\r
+\r
+ setMenuBar(alignFrameMenuBar);\r
+\r
+ MenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++)\r
+ {\r
+\r
+ item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.\r
+ elementAt(\r
+ i));\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+\r
+\r
+ fileMenu.setLabel("File");\r
+ closeMenuItem.setLabel("Close");\r
+ closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ closeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ editMenu.setLabel("Edit");\r
+ viewMenu.setLabel("View");\r
+ colourMenu.setLabel("Colour");\r
+ calculateMenu.setLabel("Calculate");\r
+ selectAllSequenceMenuItem.setLabel("Select all");\r
+ selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ selectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ deselectAllSequenceMenuItem.setLabel("Deselect All");\r
+ deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deselectAllSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ invertSequenceMenuItem.setLabel("Invert Selection");\r
+ invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ invertSequenceMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2LeftMenuItem.setLabel("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2LeftMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ remove2RightMenuItem.setLabel("Remove Right");\r
+ remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ remove2RightMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeGappedColumnMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeAllGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ viewBoxesMenuItem.setLabel("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ viewBoxesMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ viewTextMenuItem.setLabel("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ viewTextMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortPairwiseMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortIDMenuItem.setLabel("by ID");\r
+ sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortIDMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ sortGroupMenuItem.setLabel("by Group");\r
+ sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ sortGroupMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ removeRedundancyMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pairwiseAlignmentMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ PCAMenuItem.setLabel("Principal Component Analysis");\r
+ PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PCAMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ averageDistanceTreeMenuItem.setLabel(\r
+ "Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ averageDistanceTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
+ neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ neighbourTreeMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setLabel("Output to Textbox");\r
+ clustalColour.setLabel("Clustalx");\r
+\r
+ clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ clustalColour_actionPerformed(e);\r
+ }\r
+ });\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ zappoColour_actionPerformed(e);\r
+ }\r
+ });\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ taylorColour_actionPerformed(e);\r
+ }\r
+ });\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ hydrophobicityColour_actionPerformed(e);\r
+ }\r
+ });\r
+ helixColour.setLabel("Helix Propensity");\r
+ helixColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ helixColour_actionPerformed(e);\r
+ }\r
+ });\r
+ strandColour.setLabel("Strand Propensity");\r
+ strandColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ strandColour_actionPerformed(e);\r
+ }\r
+ });\r
+ turnColour.setLabel("Turn Propensity");\r
+ turnColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ turnColour_actionPerformed(e);\r
+ }\r
+ });\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ buriedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ userDefinedColour.setLabel("User Defined...");\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ userDefinedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ PIDColour_actionPerformed(e);\r
+ }\r
+ });\r
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ BLOSUM62Colour_actionPerformed(e);\r
+ }\r
+ });\r
+ avDistanceTreeBlosumMenuItem.setLabel(\r
+ "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ avTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ njTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ annotationPanelMenuItem.setActionCommand("");\r
+ annotationPanelMenuItem.setState(true);\r
+ annotationPanelMenuItem.setLabel("Show Annotations");\r
+ annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ annotationPanelMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ colourTextMenuItem.setLabel("Colour Text");\r
+ colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ colourTextMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ overviewMenuItem.setLabel("Overview Window");\r
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ overviewMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ undoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ redoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ conservationMenuItem.setLabel("by Conservation");\r
+ conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ conservationMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ noColourmenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ wrapMenuItem.setLabel("Wrap");\r
+ wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ wrapMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ renderGapsMenuItem.setLabel("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ renderGapsMenuItem_actionPerformed(null);\r
+ }\r
+ });\r
+ findMenuItem.setLabel("Find...");\r
+ findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ searchMenu.setLabel("Search");\r
+\r
+ abovePIDThreshold.setLabel("Above Identity Threshold");\r
+ abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ abovePIDThreshold_actionPerformed(null);\r
+ }\r
+ });\r
+ nucleotideColour.setLabel("Nucleotide");\r
+ nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ nucleotideColour_actionPerformed(e);\r
+ }\r
+ });\r
+ deleteGroups.setLabel("Undefine Groups");\r
+ deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ deleteGroups_actionPerformed(e);\r
+ }\r
+ });\r
+ copy.setLabel("Copy");\r
+ copy.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ copy_actionPerformed(e);\r
+ }\r
+ });\r
+ cut.setLabel("Cut");\r
+ cut.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cut_actionPerformed(e);\r
+ }\r
+ });\r
+ delete.setLabel("Delete");\r
+ delete.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ delete_actionPerformed(e);\r
+ }\r
+ });\r
+ Menu1.setLabel("Paste");\r
+ pasteNew.setLabel("To New Alignment");\r
+ pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteNew_actionPerformed(e);\r
+ }\r
+ });\r
+ pasteThis.setLabel("Add To This Alignment");\r
+ pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ pasteThis_actionPerformed(e);\r
+ }\r
+ });\r
+ applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ applyToAllGroups_actionPerformed(null);\r
+ }\r
+ });\r
+ font.setLabel("Font...");\r
+ font.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ font_actionPerformed(e);\r
+ }\r
+ });\r
+ scaleAbove.setLabel("Scale Above");\r
+ scaleAbove.setState(true);\r
+ scaleAbove.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleAbove_actionPerformed(null);\r
+ }\r
+ });\r
+ scaleLeft.setEnabled(false);\r
+ scaleLeft.setState(true);\r
+ scaleLeft.setLabel("Scale Left");\r
+ scaleLeft.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleLeft_actionPerformed(null);\r
+ }\r
+ });\r
+ scaleRight.setEnabled(false);\r
+ scaleRight.setState(true);\r
+ scaleRight.setLabel("Scale Right");\r
+ scaleRight.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ scaleRight_actionPerformed(null);\r
+ }\r
+ });\r
+ modifyPID.setLabel("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyPID_actionPerformed(e);\r
+ }\r
+ });\r
+ modifyConservation.setLabel("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ modifyConservation_actionPerformed(e);\r
+ }\r
+ });\r
+ sortByTreeMenu.setLabel("By Tree Order");\r
+ sort.setLabel("Sort");\r
+ calculate.setLabel("Calculate Tree");\r
+ inputText.setLabel("Input from textbox");\r
+ inputText.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ inputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ helpMenu.setLabel("Help");\r
+ documentation.setLabel("Documentation");\r
+ documentation.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ documentation_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ about.setLabel("About...");\r
+ about.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ about_actionPerformed(e);\r
+ }\r
+ });\r
+ seqLimits.setState(true);\r
+ seqLimits.setLabel("Show Sequence Limits");\r
+ seqLimits.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ seqLimits_itemStateChanged(e);\r
+ }\r
+ });\r
+\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(searchMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(helpMenu);\r
+ fileMenu.add(inputText);\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(Menu1);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(selectAllSequenceMenuItem);\r
+ editMenu.add(deselectAllSequenceMenuItem);\r
+ editMenu.add(invertSequenceMenuItem);\r
+ editMenu.add(deleteGroups);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ searchMenu.add(findMenuItem);\r
+ viewMenu.add(font);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(seqLimits);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(wrapMenuItem);\r
+ viewMenu.add(scaleAbove);\r
+ viewMenu.add(scaleLeft);\r
+ viewMenu.add(scaleRight);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(viewBoxesMenuItem);\r
+ viewMenu.add(viewTextMenuItem);\r
+ viewMenu.add(colourTextMenuItem);\r
+ viewMenu.add(renderGapsMenuItem);\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\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(nucleotideColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ this.add(statusBar, BorderLayout.SOUTH);\r
+ Menu1.add(pasteNew);\r
+ Menu1.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortByTreeMenu);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ helpMenu.add(documentation);\r
+ helpMenu.add(about);\r
+ }\r
}\r
+\r
int startSeq;\r
int endSeq;\r
\r
- boolean showFullId = true;\r
+ boolean showJVSuffix = true;\r
boolean showText = true;\r
boolean showColourText = false;\r
boolean showBoxes = true;\r
String param = applet.getParameter("showFullId");\r
if (param != null)\r
{\r
- showFullId = Boolean.valueOf(param).booleanValue();\r
+ showJVSuffix = Boolean.valueOf(param).booleanValue();\r
}\r
\r
param = applet.getParameter("showAnnotation");\r
return colourAppliesToAllGroups;\r
}\r
\r
- public boolean getShowFullId()\r
+ public boolean getShowJVSuffix()\r
{\r
- return showFullId;\r
+ return showJVSuffix;\r
}\r
\r
- public void setShowFullId(boolean b)\r
+ public void setShowJVSuffix(boolean b)\r
{\r
- showFullId = b;\r
+ showJVSuffix = b;\r
}\r
\r
public boolean getShowAnnotation()\r
import java.awt.event.*;\r
\r
import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
\r
-public class AlignmentPanel\r
- extends GAlignmentPanel implements AdjustmentListener\r
+public class AlignmentPanel extends Panel implements AdjustmentListener\r
{\r
\r
AlignViewport av;\r
\r
public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
{\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
if(System.getProperty("os.name").startsWith("Mac"))\r
MAC = true;\r
\r
while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
{\r
SequenceI s = al.getSequenceAt(i);\r
- if (av.getShowFullId())\r
- {\r
- id = s.getDisplayId();\r
- }\r
- else\r
- {\r
- id = s.getName();\r
- }\r
+ id = s.getDisplayId(av.getShowJVSuffix());\r
\r
if (fm.stringWidth(id) > idWidth)\r
{\r
{\r
int max = av.alignment.getWidth() /\r
seqPanel.seqCanvas.\r
- getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);\r
+ getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +1;\r
vscroll.setMaximum(max);\r
vscroll.setUnitIncrement(1);\r
vscroll.setVisibleAmount(1);\r
scalePanel.repaint();\r
annotationPanel.repaint();\r
\r
+ if (getBounds() == g.getClipBounds())\r
+ {\r
+ if (overviewPanel != null)\r
+ overviewPanel.updateOverviewImage();\r
+ }\r
+\r
+ }\r
+\r
+ protected Panel sequenceHolderPanel = new Panel();\r
+ protected Scrollbar vscroll = new Scrollbar();\r
+ protected Scrollbar hscroll = new Scrollbar();\r
+ protected Panel seqPanelHolder = new Panel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout3 = new BorderLayout();\r
+ protected Panel scalePanelHolder = new Panel();\r
+ protected Panel idPanelHolder = new Panel();\r
+ BorderLayout borderLayout5 = new BorderLayout();\r
+ protected Panel idSpaceFillerPanel1 = new Panel();\r
+ public Panel annotationSpaceFillerHolder = new Panel();\r
+ BorderLayout borderLayout6 = new BorderLayout();\r
+ BorderLayout borderLayout7 = new BorderLayout();\r
+ Panel hscrollHolder = new Panel();\r
+ BorderLayout borderLayout10 = new BorderLayout();\r
+ protected Panel hscrollFillerPanel = new Panel();\r
+ BorderLayout borderLayout11 = new BorderLayout();\r
+ public Panel annotationScroller = new Panel();\r
+ BorderLayout borderLayout4 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+\r
+ private void jbInit() throws Exception {\r
+ // idPanelHolder.setPreferredSize(new Dimension(70, 10));\r
+ this.setLayout(borderLayout7);\r
+\r
+ // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));\r
+ sequenceHolderPanel.setLayout(borderLayout3);\r
+ seqPanelHolder.setLayout(borderLayout1);\r
+ scalePanelHolder.setBackground(Color.white);\r
+\r
+ // scalePanelHolder.setPreferredSize(new Dimension(10, 30));\r
+ scalePanelHolder.setLayout(borderLayout6);\r
+ idPanelHolder.setLayout(borderLayout5);\r
+ idSpaceFillerPanel1.setBackground(Color.white);\r
+\r
+ // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));\r
+ idSpaceFillerPanel1.setLayout(borderLayout11);\r
+ annotationSpaceFillerHolder.setBackground(Color.white);\r
+\r
+ // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));\r
+ annotationSpaceFillerHolder.setLayout(borderLayout4);\r
+ hscroll.setOrientation(Scrollbar.HORIZONTAL);\r
+ hscrollHolder.setLayout(borderLayout10);\r
+ hscrollFillerPanel.setBackground(Color.white);\r
+\r
+ // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));\r
+ hscrollHolder.setBackground(Color.white);\r
+\r
+ // annotationScroller.setPreferredSize(new Dimension(10, 80));\r
+ // this.setPreferredSize(new Dimension(220, 166));\r
+ seqPanelHolder.setBackground(Color.white);\r
+ idPanelHolder.setBackground(Color.white);\r
+ annotationScroller.setLayout(borderLayout2);\r
+ sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);\r
+ sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);\r
+ seqPanelHolder.add(vscroll, BorderLayout.EAST);\r
+ sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);\r
+\r
+ // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);\r
+ this.add(idPanelHolder, BorderLayout.WEST);\r
+ idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);\r
+ idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);\r
+ this.add(hscrollHolder, BorderLayout.SOUTH);\r
+ hscrollHolder.add(hscroll, BorderLayout.CENTER);\r
+ hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);\r
+ this.add(sequenceHolderPanel, BorderLayout.CENTER);\r
}\r
+\r
}\r
\r
import jalview.datamodel.*;\r
import jalview.io.*;\r
-import jalview.jbappletgui.*;\r
\r
-public class CutAndPasteTransfer\r
- extends GCutAndPasteTransfer\r
+public class CutAndPasteTransfer extends Panel\r
{\r
jalview.bin.JalviewLite applet;\r
+\r
+ boolean pdbImport = false;\r
+ Sequence seq;\r
+ SeqCanvas seqcanvas;\r
+\r
public CutAndPasteTransfer(boolean forImport, jalview.bin.JalviewLite mainApplet)\r
{\r
- super();\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
+\r
applet = mainApplet;\r
\r
if (!forImport)\r
}\r
}\r
\r
+ public void setPDBImport(Sequence seq, SeqCanvas seqcanvas)\r
+ {\r
+ this.seq = seq;\r
+ this.seqcanvas = seqcanvas;\r
+ pdbImport = true;\r
+ }\r
+\r
+\r
public String getText()\r
{\r
return textarea.getText();\r
+warning);\r
\r
textarea.setCaretPosition(text.length());\r
- return;\r
}\r
\r
- SequenceI[] sequences = null;\r
+ if(pdbImport)\r
+ {\r
+ new MCview.AppletPDBViewer(text, "Paste", seq, seqcanvas);\r
+ }\r
+ else\r
+ {\r
+ SequenceI[] sequences = null;\r
\r
- String format = IdentifyFile.Identify(text, "Paste");\r
- sequences = new FormatAdapter().readFile(text, "Paste", format);\r
+ String format = IdentifyFile.Identify(text, "Paste");\r
+ sequences = new AppletFormatAdapter().readFile(text, "Paste", format);\r
\r
- if (sequences != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences), applet,\r
- "Cut & Paste input - " + format);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
+ if (sequences != null)\r
+ {\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences), applet,\r
+ "Cut & Paste input - " + format);\r
+ af.statusBar.setText("Successfully pasted alignment file");\r
+ }\r
}\r
\r
- Frame frame = (Frame)this.getParent();\r
- frame.setVisible(false);\r
+ ((Frame)this.getParent()).setVisible(false);\r
}\r
\r
protected void cancel_actionPerformed(ActionEvent e)\r
{\r
- Frame frame = (Frame)this.getParent();\r
- frame.setVisible(false);\r
+ ((Frame)this.getParent()).setVisible(false);\r
+ }\r
+\r
+ protected TextArea textarea = new TextArea();\r
+ Button ok = new Button();\r
+ Button cancel = new Button();\r
+ protected Panel buttonPanel = new Panel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+\r
+ private void jbInit() throws Exception {\r
+ textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));\r
+ textarea.setText("Paste your alignment file here");\r
+ textarea.addMouseListener(new java.awt.event.MouseAdapter() {\r
+ public void mousePressed(MouseEvent e) {\r
+ textarea_mousePressed(e);\r
+ }\r
+ });\r
+ this.setLayout(borderLayout1);\r
+ ok.setLabel("OK");\r
+ ok.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ ok_actionPerformed(e);\r
+ }\r
+ });\r
+ cancel.setLabel("Cancel");\r
+ cancel.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancel_actionPerformed(e);\r
+ }\r
+ });\r
+ this.add(buttonPanel, BorderLayout.SOUTH);\r
+ buttonPanel.add(ok, null);\r
+ buttonPanel.add(cancel, null);\r
+ this.add(textarea, java.awt.BorderLayout.CENTER);\r
}\r
\r
+ void textarea_mousePressed(MouseEvent e) {\r
+ if (textarea.getText().startsWith("Paste your")) {\r
+ textarea.setText("");\r
+ }\r
+ }\r
}\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 java.util.*;\r
+import jalview.datamodel.*;\r
\r
import java.awt.*;\r
\r
-import jalview.datamodel.*;\r
+import java.util.*;\r
+\r
\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class FeatureRenderer\r
{\r
- AlignViewport av;\r
-\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup[] allGroups = null;\r
- Color resBoxColour;\r
- Graphics graphics;\r
-\r
- public FeatureRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
- public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
- int start, int end, int x1, int y1, int width,\r
- int height)\r
- {\r
- Vector features = seq.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- while (e.hasMoreElements())\r
+ AlignViewport av;\r
+ SequenceGroup currentSequenceGroup = null;\r
+ SequenceGroup[] allGroups = null;\r
+ Color resBoxColour;\r
+ Graphics graphics;\r
+ float transparency = .4f;\r
+\r
+ // The following vector holds the features which are\r
+ // to be added, in the correct order or rendering\r
+ Vector featuresDisplayed;\r
+\r
+ /**\r
+ * Creates a new FeatureRenderer object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public FeatureRenderer(AlignViewport av)\r
{\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- if (sf.getStart() > seq.getEnd())\r
- {\r
- continue;\r
- }\r
+ this.av = av;\r
+ initColours();\r
+ String version = System.getProperty("java.version");\r
+ if (version.indexOf("1.1") == 0)\r
+ highlightTransparent = false;\r
\r
- int fstart = seq.findIndex(sf.getStart()) - 1;\r
- int fend = seq.findIndex(sf.getEnd()) - 1;\r
+ }\r
\r
- if ( (fstart <= end && fend >= start))\r
- {\r
- if (fstart < 0) // fix for if the feature we have starts before the sequence start,\r
+boolean highlightTransparent = true;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ * @param sg DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
+ int start, int end, int x1, int y1, int width, int height)\r
+ {\r
+\r
+ if(seq.getSequenceFeatures()==null)\r
+ return;\r
+\r
+ Enumeration e = null, e2;\r
+ String type;\r
+ if(featuresDisplayed!=null)\r
+ e = featuresDisplayed.elements();\r
+ else\r
+ e = seq.getSequenceFeatures().elements();\r
+\r
+ if(highlightTransparent)\r
{\r
- fstart = 0; // but the feature end is still valid!!\r
+ // MyGraphics.SetTransparency(g, transparency);\r
}\r
\r
- if (fstart == fend)\r
- {\r
- g.setColor(Color.red);\r
- g.fillRoundRect( (fstart - start) * width, y1, width, height, 4, 4);\r
- g.setColor(Color.white);\r
-\r
- char s = seq.getSequence().charAt(fstart);\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (fstart - start),\r
- y1 + height - pady);\r
\r
- }\r
- else\r
+ while (e.hasMoreElements())\r
{\r
- for (int i = fstart; i <= fend; i++)\r
- {\r
- char s = seq.getSequence().charAt(i);\r
- if (jalview.util.Comparison.isGap(s))\r
+ SequenceFeature sf=null;\r
+ if(featuresDisplayed!=null)\r
+ {\r
+ e2 = seq.getSequenceFeatures().elements();\r
+ type = e.nextElement().toString();\r
+ while(e2.hasMoreElements())\r
+ {\r
+ sf = (SequenceFeature) e2.nextElement();\r
+ if(sf.getType().equals(type))\r
+ break;\r
+ else\r
+ sf = null;\r
+ }\r
+ }\r
+ else\r
{\r
+ sf = (SequenceFeature) e.nextElement();\r
+ type = sf.getType();\r
+ }\r
+\r
+ if(sf==null)\r
continue;\r
+\r
+\r
+ if (sf.getBegin() > seq.getEnd())\r
+ {\r
+ continue;\r
}\r
\r
- g.setColor(Color.blue);\r
- g.fillRect( (i - start) * width, y1, width, height);\r
+ int fstart = seq.findIndex(sf.getBegin()) - 1;\r
+ int fend = seq.findIndex(sf.getEnd()) - 1;\r
+\r
+ if (((fstart <= end) && (fend >= start)))\r
+ {\r
+ if (fstart < start)\r
+ { // fix for if the feature we have starts before the sequence start,\r
+ fstart = start; // but the feature end is still valid!!\r
+ }\r
\r
- g.setColor(Color.white);\r
+ if (fend >= end)\r
+ {\r
+ fend = end;\r
+ }\r
\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + width * (i - start),\r
- y1 + height - pady);\r
+ if (fstart == fend)\r
+ {\r
+ g.setColor(getColour(type));\r
+ g.fillRoundRect((fstart - start) * width, y1, width,\r
+ height, 4, 4);\r
+ g.setColor(Color.white);\r
+\r
+ char s = seq.getSequence().charAt(fstart);\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int charOffset = (width - fm.charWidth(s)) / 2;\r
+ int pady = height / 5;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (fstart - start)),\r
+ (y1 + height) - pady);\r
+ }\r
+ else\r
+ {\r
+ for (int i = fstart; i <= fend; i++)\r
+ {\r
+ char s = seq.getSequence().charAt(i);\r
+\r
+ if (jalview.util.Comparison.isGap(s))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ g.setColor(getColour(type));\r
+ g.fillRect((i - start) * width, y1, width, height);\r
+\r
+ g.setColor(Color.white);\r
+\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int charOffset = (width - fm.charWidth(s)) / 2;\r
+ int pady = height / 5;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (i - start)),\r
+ (y1 + height) - pady);\r
+ }\r
+ }\r
+ }\r
}\r
- }\r
+\r
+ if (highlightTransparent)\r
+ {\r
+ // MyGraphics.SetTransparency(g, 1.0f);\r
+ }\r
+ }\r
+\r
+ public Color getColour(String featureType)\r
+ {\r
+ return (Color)featureColours.get(featureType);\r
+ }\r
+\r
+ public void setColour(String featureType, Color col)\r
+ {\r
+ featureColours.put(featureType, col);\r
+ }\r
+\r
+ public void setTransparency(float value)\r
+ {\r
+ transparency = value;\r
+ }\r
+\r
+ public float getTransparency()\r
+ {\r
+ return transparency;\r
+ }\r
+\r
+ public void setFeaturePriority(Object [][] data)\r
+ {\r
+ // The feature table will display high priority\r
+ // features at the top, but theses are the ones\r
+ // we need to render last, so invert the data\r
+ featuresDisplayed = new Vector();\r
+ for(int i=data.length-1; i>-1; i--)\r
+ {\r
+ String type = data[i][0].toString();\r
+ setColour(type, (Color)data[i][1]);\r
+ if( ((Boolean)data[i][2]).booleanValue() )\r
+ featuresDisplayed.addElement(type);\r
}\r
+ }\r
\r
+ Hashtable featureColours = new Hashtable();\r
+ void initColours()\r
+ {\r
+ featureColours.put("active site", new Color(255, 75, 0));\r
+ featureColours.put("binding site", new Color(245, 85, 0));\r
+ featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
+ featureColours.put("chain", new Color(225, 105, 0));\r
+ featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
+ featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
+ featureColours.put("cross-link", new Color(195, 135, 0));\r
+ featureColours.put("disulfide bond", new Color(185, 145, 0));\r
+ featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
+ featureColours.put("domain", new Color(165, 165, 0));\r
+ featureColours.put("glycosylation site", new Color(155, 175, 0));\r
+ featureColours.put("helix", new Color(145, 185, 0));\r
+ featureColours.put("initiator methionine", new Color(135, 195, 5));\r
+ featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
+ featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
+ featureColours.put("modified residue", new Color(105, 225, 35));\r
+ featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
+ featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
+ featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
+ featureColours.put("nucleotide phosphate-binding region",\r
+ new Color(65, 245, 75));\r
+ featureColours.put("peptide", new Color(55, 235, 85));\r
+ featureColours.put("propeptide", new Color(45, 225, 95));\r
+ featureColours.put("region of interest", new Color(35, 215, 105));\r
+ featureColours.put("repeat", new Color(25, 205, 115));\r
+ featureColours.put("selenocysteine", new Color(15, 195, 125));\r
+ featureColours.put("sequence conflict", new Color(5, 185, 135));\r
+ featureColours.put("sequence variant", new Color(0, 175, 145));\r
+ featureColours.put("short sequence motif", new Color(0, 165, 155));\r
+ featureColours.put("signal peptide", new Color(0, 155, 165));\r
+ featureColours.put("site", new Color(0, 145, 175));\r
+ featureColours.put("splice variant", new Color(0, 135, 185));\r
+ featureColours.put("strand", new Color(0, 125, 195));\r
+ featureColours.put("topological domain", new Color(0, 115, 205));\r
+ featureColours.put("transit peptide", new Color(0, 105, 215));\r
+ featureColours.put("transmembrane region", new Color(0, 95, 225));\r
+ featureColours.put("turn", new Color(0, 85, 235));\r
+ featureColours.put("unsure residue", new Color(0, 75, 245));\r
+ featureColours.put("zinc finger region", new Color(0, 65, 255));\r
}\r
- }\r
\r
}\r
+\r
+\r
+\r
import java.awt.event.*;\r
\r
import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
\r
-public class Finder\r
- extends GFinder\r
+public class Finder extends Panel\r
{\r
AlignViewport av;\r
AlignmentPanel ap;\r
int resIndex = 0;\r
public Finder(final AlignmentPanel ap)\r
{\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
this.av = ap.av;\r
this.ap = ap;\r
frame = new Frame();\r
\r
}\r
\r
+ Label jLabel1 = new Label();\r
+ protected TextField textfield = new TextField();\r
+ protected Button findAll = new Button();\r
+ protected Button findNext = new Button();\r
+ Panel jPanel1 = new Panel();\r
+ GridLayout gridLayout1 = new GridLayout();\r
+ protected Button createNewGroup = new Button();\r
+\r
+\r
+ private void jbInit() throws Exception {\r
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel1.setText("Find");\r
+ jLabel1.setBounds(new Rectangle(3, 30, 34, 15));\r
+ this.setLayout(null);\r
+ textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ textfield.setText("");\r
+ textfield.setBounds(new Rectangle(40, 27, 133, 21));\r
+ textfield.addKeyListener(new java.awt.event.KeyAdapter() {\r
+ public void keyTyped(KeyEvent e) {\r
+ textfield_keyTyped(e);\r
+ }\r
+ });\r
+ textfield.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ textfield_actionPerformed(e);\r
+ }\r
+ });\r
+ findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ findAll.setLabel("Find all");\r
+ findAll.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findAll_actionPerformed(e);\r
+ }\r
+ });\r
+ findNext.setEnabled(false);\r
+ findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ findNext.setLabel("Find Next");\r
+ findNext.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ findNext_actionPerformed(e);\r
+ }\r
+ });\r
+ jPanel1.setBounds(new Rectangle(180, 5, 141, 64));\r
+ jPanel1.setLayout(gridLayout1);\r
+ gridLayout1.setHgap(0);\r
+ gridLayout1.setRows(3);\r
+ gridLayout1.setVgap(2);\r
+ createNewGroup.setEnabled(false);\r
+ createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ createNewGroup.setLabel("Create new group");\r
+ createNewGroup.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ createNewGroup_actionPerformed(e);\r
+ }\r
+ });\r
+ jPanel1.add(findNext, null);\r
+ jPanel1.add(findAll, null);\r
+ jPanel1.add(createNewGroup, null);\r
+ this.add(textfield, null);\r
+ this.add(jLabel1, null);\r
+ this.add(jPanel1, null);\r
+ }\r
+\r
+ void textfield_keyTyped(KeyEvent e) {\r
+ findNext.setEnabled(true);\r
+ }\r
+\r
}\r
\r
import java.awt.*;\r
\r
-import jalview.jbappletgui.*;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ItemEvent;\r
\r
public class FontChooser\r
- extends GFontChooser\r
+ extends Panel\r
{\r
AlignmentPanel ap;\r
TreePanel tp;\r
\r
public FontChooser(TreePanel tp)\r
{\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
this.tp = tp;\r
oldFont = tp.getTreeFont();\r
init();\r
}\r
changeFont();\r
}\r
+ Label label1 = new Label();\r
+ protected Choice fontSize = new Choice();\r
+ protected Choice fontStyle = new Choice();\r
+ Label label2 = new Label();\r
+ Label label3 = new Label();\r
+ protected Choice fontName = new Choice();\r
+ Button ok = new Button();\r
+ Button cancel = new Button();\r
+ Panel panel1 = new Panel();\r
+ Panel panel2 = new Panel();\r
+ Panel panel3 = new Panel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+ BorderLayout borderLayout3 = new BorderLayout();\r
+ Panel panel4 = new Panel();\r
+ Panel panel5 = new Panel();\r
+ BorderLayout borderLayout4 = new BorderLayout();\r
+\r
+\r
+ private void jbInit() throws Exception {\r
+ label1.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ label1.setAlignment(Label.RIGHT);\r
+ label1.setText("Font: ");\r
+ this.setLayout(borderLayout4);\r
+ fontSize.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ fontSize.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fontSize_actionPerformed();\r
+ }\r
+ });\r
+ fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ fontStyle.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fontStyle_actionPerformed();\r
+ }\r
+ });\r
+ label2.setAlignment(Label.RIGHT);\r
+ label2.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ label2.setText("Size: ");\r
+ label3.setAlignment(Label.RIGHT);\r
+ label3.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ label3.setText("Style: ");\r
+ fontName.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ fontName.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fontName_actionPerformed();\r
+ }\r
+ });\r
+ ok.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ ok.setLabel("OK");\r
+ ok.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ ok_actionPerformed();\r
+ }\r
+ });\r
+ cancel.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ cancel.setLabel("Cancel");\r
+ cancel.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancel_actionPerformed();\r
+ }\r
+ });\r
+ this.setBackground(Color.white);\r
+ panel1.setLayout(borderLayout1);\r
+ panel2.setLayout(borderLayout3);\r
+ panel3.setLayout(borderLayout2);\r
+ panel5.setBackground(Color.white);\r
+ panel4.setBackground(Color.white);\r
+ panel1.setBackground(Color.white);\r
+ panel2.setBackground(Color.white);\r
+ panel3.setBackground(Color.white);\r
+ panel1.add(label1, BorderLayout.WEST);\r
+ panel1.add(fontName, BorderLayout.CENTER);\r
+ panel5.add(panel1, null);\r
+ panel5.add(panel3, null);\r
+ panel5.add(panel2, null);\r
+ panel2.add(label3, BorderLayout.WEST);\r
+ panel2.add(fontStyle, BorderLayout.CENTER);\r
+ panel3.add(label2, BorderLayout.WEST);\r
+ panel3.add(fontSize, BorderLayout.CENTER);\r
+ this.add(panel4, BorderLayout.SOUTH);\r
+ panel4.add(ok, null);\r
+ panel4.add(cancel, null);\r
+ this.add(panel5, BorderLayout.CENTER);\r
+ }\r
\r
}\r
gg.setColor(Color.black);\r
}\r
\r
- String string = s.getName();\r
- if (av.getShowFullId())\r
- {\r
- string = s.getDisplayId();\r
- }\r
\r
- gg.drawString(string, 0,\r
+ gg.drawString( s.getDisplayId(av.getShowJVSuffix()), 0,\r
((i - starty) * charHeight) + ypos +\r
charHeight - (charHeight / 5));\r
\r
av.charHeight);\r
\r
gg.setColor(currentTextColor);\r
- String string = av.alignment.getSequenceAt(i).getName();\r
- if (av.getShowFullId())\r
- {\r
- string = av.alignment.getSequenceAt(i).getDisplayId();\r
- }\r
- gg.drawString(string, 0,\r
+\r
+ gg.drawString(av.alignment.getSequenceAt(i)\r
+ .getDisplayId(av.getShowJVSuffix()), 0,\r
((i - starty) * av.charHeight) +\r
av.charHeight - (av.charHeight / 5));\r
}\r
//DEFAULT LINK IS FIRST IN THE LINK LIST\r
int seq = av.getIndex(y);\r
String id = av.getAlignment().getSequenceAt(seq).getName();\r
+ if (id.indexOf("|") > -1)\r
+ id = id.substring(id.lastIndexOf("|") + 1);\r
\r
String target = links.elementAt(0).toString();\r
target = target.substring(0, target.indexOf("|"));\r
\r
try\r
{\r
- jalview.bin.JalviewLite.showURL(url, target);\r
+\r
+ alignPanel.alignFrame.showURL(url, target);\r
}\r
catch (Exception ex)\r
{\r
\r
// Can set different properties in this seqCanvas than\r
// main visible SeqCanvas\r
- SeqCanvas overviewSeq;\r
+ SequenceRenderer sr;\r
+ //FeatureRenderer fr;\r
\r
\r
Frame nullFrame;\r
nullFrame = new Frame();\r
nullFrame.addNotify();\r
\r
- overviewSeq = new SeqCanvas(av);\r
- overviewSeq.isOverview = true;\r
- overviewSeq.sr.renderGaps = false;\r
+\r
+ sr = new SequenceRenderer(av);\r
+ sr.graphics = nullFrame.getGraphics();\r
+ sr.renderGaps( false );\r
+ //fr = new FeatureRenderer(av);\r
+ //fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
+ //fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;\r
+\r
\r
\r
// scale the initial size of overviewpanel to shape of alignment\r
float sampleCol = (float) alwidth / (float) width;\r
float sampleRow = (float) alheight / (float) sequencesHeight;\r
\r
+ int lastcol=-1, lastrow=-1;\r
+ Color color = Color.white;\r
for (int col = 0; col < width; col++)\r
{\r
for (int row = 0; row < sequencesHeight; row++)\r
{\r
- overviewSeq.drawPanel(mg,\r
- (int) (col * sampleCol),\r
- (int) (col * sampleCol),\r
- (int) (row * sampleRow),\r
- (int) (row * sampleRow) + 1,\r
- (int) (col * sampleCol),\r
- (int) (row * sampleRow), 0);\r
- mg.translate(0, 1);\r
+ if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
+ {\r
+ mg.setColor(color);\r
+ mg.fillRect(col,row,1,1);\r
+ continue;\r
+ }\r
+\r
+ lastrow = (int)(row*sampleRow);\r
+ lastcol = (int)(col*sampleCol);\r
+\r
+ color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);\r
+\r
+ mg.setColor(color);\r
+ mg.fillRect(col,row,1,1);\r
\r
if (av.conservation != null)\r
+ {\r
+ mg.translate(col, sequencesHeight);\r
ap.annotationPanel.drawGraph(mg, av.conservation,\r
(int) (sampleCol) + 1,\r
graphHeight,\r
(int) (col * sampleCol),\r
(int) (col * sampleCol) + 1);\r
-\r
+ mg.translate(-col, -sequencesHeight);\r
+ }\r
}\r
- mg.translate(0, -sequencesHeight);\r
- mg.translate(1, 0);\r
+ }\r
\r
- }\r
System.gc();\r
\r
resizing = false;\r
\r
import jalview.analysis.*;\r
import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
+\r
\r
public class PCAPanel\r
- extends GPCAPanel implements Runnable\r
+ extends Frame implements Runnable\r
{\r
PCA pca;\r
int top;\r
\r
public PCAPanel(AlignViewport av)\r
{\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ for (int i = 1; i < 8; i++)\r
+ {\r
+ xCombobox.addItem("dim " + i);\r
+ yCombobox.addItem("dim " + i);\r
+ zCombobox.addItem("dim " + i);\r
+ }\r
+\r
this.av = av;\r
if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() > 3)\r
{\r
{\r
rc.showLabels( labels.getState() );\r
}\r
+ Panel jPanel2 = new Panel();\r
+ Label jLabel1 = new Label();\r
+ Label jLabel2 = new Label();\r
+ Label jLabel3 = new Label();\r
+ protected Choice xCombobox = new Choice();\r
+ protected Choice yCombobox = new Choice();\r
+ protected Choice zCombobox = new Choice();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ MenuBar menuBar1 = new MenuBar();\r
+ Menu menu1 = new Menu();\r
+ Menu menu2 = new Menu();\r
+ protected CheckboxMenuItem labels = new CheckboxMenuItem();\r
+ MenuItem values = new MenuItem();\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ this.setLayout(borderLayout1);\r
+ jPanel2.setLayout(flowLayout1);\r
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel1.setText("x=");\r
+ jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel2.setText("y=");\r
+ jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel3.setText("z=");\r
+ jPanel2.setBackground(Color.white);\r
+ zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ zCombobox.addItemListener(new java.awt.event.ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ zCombobox_actionPerformed(null);\r
+ }\r
+ });\r
+ yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ yCombobox.addItemListener(new java.awt.event.ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ yCombobox_actionPerformed(null);\r
+ }\r
+ });\r
+ xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ xCombobox.addItemListener(new java.awt.event.ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent e)\r
+ {\r
+ xCombobox_actionPerformed(null);\r
+ }\r
+ });\r
+ this.setMenuBar(menuBar1);\r
+ menu1.setLabel("File");\r
+ menu2.setLabel("View");\r
+ labels.setLabel("Labels");\r
+ labels.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent itemEvent)\r
+ {\r
+ labels_itemStateChanged(itemEvent);\r
+ }\r
+ });\r
+ values.setLabel("Output Values...");\r
+ values.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent actionEvent)\r
+ {\r
+ values_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+ this.add(jPanel2, BorderLayout.SOUTH);\r
+ jPanel2.add(jLabel1, null);\r
+ jPanel2.add(xCombobox, null);\r
+ jPanel2.add(jLabel2, null);\r
+ jPanel2.add(yCombobox, null);\r
+ jPanel2.add(jLabel3, null);\r
+ jPanel2.add(zCombobox, null);\r
+ menuBar1.add(menu1);\r
+ menuBar1.add(menu2);\r
+ menu2.add(labels);\r
+ menu1.add(values);\r
+ }\r
\r
}\r
\r
import jalview.analysis.*;\r
import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
+import java.awt.*;\r
\r
public class PairwiseAlignPanel\r
- extends GPairwiseAlignPanel\r
+ extends Panel\r
{\r
Vector sequences = new Vector();\r
AlignmentPanel ap;\r
\r
public PairwiseAlignPanel(AlignmentPanel ap)\r
{\r
- super();\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
this.ap = ap;\r
float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.\r
getHeight()];\r
\r
as.calcScoreMatrix();\r
as.traceAlignment();\r
- as.printAlignment();\r
+ as.printAlignment(System.out);\r
scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
totscore = totscore + scores[i][j];\r
\r
"Pairwise Aligned Sequences");\r
\r
}\r
+ protected ScrollPane scrollPane = new ScrollPane();\r
+ protected TextArea textarea = new TextArea();\r
+ protected Button viewInEditorButton = new Button();\r
+ Panel jPanel1 = new Panel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(borderLayout1);\r
+ textarea.setFont(new java.awt.Font("Monospaced", 0, 12));\r
+ textarea.setText("");\r
+ viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ viewInEditorButton.setLabel("View in alignment editor");\r
+ viewInEditorButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ viewInEditorButton_actionPerformed(e);\r
+ }\r
+ });\r
+ this.add(scrollPane, BorderLayout.CENTER);\r
+ scrollPane.add(textarea);\r
+ this.add(jPanel1, BorderLayout.SOUTH);\r
+ jPanel1.add(viewInEditorButton, null);\r
+ }\r
\r
}\r
import java.awt.event.*;\r
\r
import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
\r
-public class RedundancyPanel\r
- extends GSliderPanel\r
+public class RedundancyPanel extends SliderPanel\r
{\r
AlignmentPanel ap;\r
\r
\r
public RedundancyPanel(AlignmentPanel ap)\r
{\r
+ super(ap, 0, false, null);\r
+\r
this.ap = ap;\r
\r
label.setText("Enter the redundancy threshold");\r
RotatableMatrix idmat = new RotatableMatrix(3, 3);\r
RotatableMatrix objmat = new RotatableMatrix(3, 3);\r
RotatableMatrix rotmat = new RotatableMatrix(3, 3);\r
+ String tooltip;\r
+ int toolx, tooly;\r
\r
//RubberbandRectangle rubberband;\r
\r
return getPreferredSize();\r
}\r
\r
+ public void update(Graphics g)\r
+ {\r
+ paint(g);\r
+ }\r
public void paint(Graphics g)\r
{\r
if (points == null)\r
drawAxes(ig);\r
}\r
\r
+ if(tooltip!=null)\r
+ {\r
+ ig.setColor(Color.red);\r
+ ig.drawString(tooltip, toolx, tooly);\r
+ }\r
+\r
g.drawImage(img, 0, 0, this);\r
}\r
}\r
getName(),\r
x - 3, y - 4);\r
}\r
-\r
}\r
-// //Now the rectangle\r
-// if (rectx2 != -1 && recty2 != -1) {\r
-// g.setColor(Color.white);\r
-//\r
-// g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);\r
-// }\r
}\r
\r
public Dimension minimumsize()\r
\r
public void keyPressed(KeyEvent evt)\r
{\r
- requestFocus();\r
if (evt.getKeyCode() == KeyEvent.VK_UP)\r
{\r
scalefactor = (float) (scalefactor * 1.1);\r
repaint();\r
}\r
\r
- // private void fireSequenceSelectionEvent(Selection sel) {\r
- // controller.handleSequenceSelectionEvent(new SequenceSelectionEvent(this,sel));\r
- //}\r
\r
public void mouseMoved(MouseEvent evt)\r
{\r
- // SequenceI found = findPoint(evt.getX(), evt.getY());\r
+ SequenceI found = findPoint(evt.getX(), evt.getY());\r
+ if(found==null)\r
+ tooltip = null;\r
+ else\r
+ {\r
+ tooltip = found.getName();\r
+ toolx = evt.getX();\r
+ tooly = evt.getY();\r
+ }\r
+ repaint();\r
}\r
\r
public void mouseDragged(MouseEvent evt)\r
{\r
mx = evt.getX();\r
my = evt.getY();\r
- //Check if this is a rectangle drawing drag\r
- if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)\r
- {\r
-// rectx2 = evt.getX();\r
-// recty2 = evt.getY();\r
- }\r
- else\r
- {\r
+\r
rotmat.setIdentity();\r
\r
rotmat.rotate( (float) (my - omy), 'x');\r
omy = my;\r
\r
paint(this.getGraphics());\r
- }\r
-\r
}\r
\r
public void rectSelect(int x1, int y1, int x2, int y2)\r
return null;\r
}\r
}\r
- /* public boolean handleRubberbandEvent(RubberbandEvent evt) {\r
- System.out.println("Rubberband handler called in RotatableCanvas with " +\r
- evt.getBounds());\r
-\r
- Rubberband rb = (Rubberband)evt.getSource();\r
-\r
- // Clear the current selection (instance variable)\r
- //if ((rb.getModifiers() & Event.SHIFT_MASK) == 0) {\r
- // clearSelection();\r
- //}\r
-\r
- if (rb.getComponent() == this) {\r
- Rectangle bounds = evt.getBounds();\r
- rectSelect(bounds.x,bounds.y,bounds.x+bounds.width,bounds.y+bounds.height);\r
- }\r
-\r
- redrawneeded = true;\r
- paint(this.getGraphics());\r
-\r
- return true;\r
- }*/\r
\r
}\r
\r
boolean fastPaint = false;\r
\r
- boolean isOverview = false;\r
\r
public SeqCanvas(AlignViewport av)\r
{\r
fr = new FeatureRenderer(av);\r
sr = new SequenceRenderer(av);\r
PaintRefresher.Register(this, av.alignment);\r
+ }\r
\r
+ public AlignViewport getViewport()\r
+ {\r
+ return av;\r
+ }\r
+\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
}\r
\r
+ MCview.AppletPDBCanvas pdbCanvas;\r
+ public SequenceRenderer getSequenceRenderer()\r
+ {\r
+ return sr;\r
+ }\r
+\r
+ public void setPDBCanvas(MCview.AppletPDBCanvas pc)\r
+ {\r
+ pdbCanvas = pc;\r
+ }\r
+\r
+\r
void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
{\r
int scalestartx = startx - startx % 10 + 10;\r
\r
g.drawImage(img, 0, 0, this);\r
\r
+ if (pdbCanvas != null)\r
+ {\r
+ pdbCanvas.updateSeqColours();\r
+ }\r
}\r
\r
int LABEL_WEST, LABEL_EAST;\r
\r
if(av.showAnnotation)\r
{\r
- g.translate(0, cHeight + ypos);\r
+ g.translate(0, cHeight + ypos+4);\r
if(annotations==null)\r
annotations = new AnnotationPanel(av);\r
\r
annotations.drawComponent( g, startRes, endx + 1);\r
- g.translate(0, -cHeight - ypos);\r
+ g.translate(0, -cHeight - ypos-4);\r
}\r
g.translate(-LABEL_WEST, 0);\r
\r
group = (SequenceGroup) groups.elementAt(0);\r
groupIndex = 0;\r
}\r
- if (group != null && !isOverview)\r
+ if (group != null)\r
{\r
do\r
{\r
group.sequences.contains(av.alignment.getSequenceAt(\r
i)))\r
{\r
- if ((bottom == -1) &&\r
- !group.sequences.contains(\r
- av.alignment.getSequenceAt(i + 1)))\r
- {\r
+\r
+ if (bottom == -1)\r
+ {\r
+ if(i == y2-1 || // Dont check for i+1 if on the bottom row\r
+ !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))\r
+\r
bottom = sy + av.charHeight;\r
}\r
\r
}\r
}\r
\r
- ap.alignFrame.statusBar.setText(text.toString());\r
+ if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
+ {\r
+ seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
+ }\r
+\r
\r
// use aa to see if the mouse pointer is on a\r
- if (av.showSequenceFeatures)\r
+ if (av.showSequenceFeatures && sequence.getSequenceFeatures()!=null)\r
{\r
Vector features = sequence.getSequenceFeatures();\r
Enumeration e = features.elements();\r
- StringBuffer sbuffer = new StringBuffer();\r
+ text.append(" Sequence Feature: ");\r
\r
while (e.hasMoreElements())\r
{\r
SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- if (sf.getStart() <= sequence.findPosition(res) &&\r
+ if (sf.getBegin() <= sequence.findPosition(res) &&\r
sf.getEnd() >= sequence.findPosition(res))\r
{\r
- if (sbuffer.length() > 0)\r
- {\r
- sbuffer.append("; ");\r
- }\r
- sbuffer.append(sf.getType() + " " + sf.getDescription());\r
+ text.append(sf.getDescription());\r
if (sf.getStatus().length() > 0)\r
{\r
- sbuffer.append(" (" + sf.getStatus() + ")");\r
+ text.append(" (" + sf.getStatus() + ")");\r
}\r
+ text.append("; ");\r
}\r
\r
}\r
}\r
\r
+ ap.alignFrame.statusBar.setText(text.toString());\r
+\r
}\r
\r
public void doMouseDragged(MouseEvent evt)\r
oldSeq = seq;\r
startWrapBlock=wrappedBlock;\r
\r
+ if(seq==-1)\r
+ return;\r
+\r
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
\r
if (sequence == null || res > sequence.getLength())\r
renderGaps = b;\r
}\r
\r
- public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
+ public Color getResidueBoxColour(SequenceI seq, int i)\r
{\r
- getBoxColour(cs, seq, i);\r
+ allGroups = av.alignment.findAllGroups(seq);\r
+\r
+ if (inCurrentSequenceGroup(i))\r
+ {\r
+ if (currentSequenceGroup.getDisplayBoxes())\r
+ {\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ }\r
+ }\r
+ else if (av.getShowBoxes())\r
+ {\r
+ getBoxColour(av.globalColourScheme, seq, i);\r
+ }\r
+\r
return resBoxColour;\r
- }\r
+ }\r
\r
void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
{\r
}\r
}\r
\r
+ Image offscreen;\r
+ public Color findSequenceColour(SequenceI seq, int i)\r
+ {\r
+ allGroups = av.alignment.findAllGroups(seq);\r
+ drawBoxes(seq, i,i, 0, 0, 1,1);\r
+ return resBoxColour;\r
+ }\r
+\r
public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
int start, int end, int x1, int y1, int width,\r
int height)\r
import java.awt.event.*;\r
\r
import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
import jalview.schemes.*;\r
\r
-public class SliderPanel\r
- extends GSliderPanel\r
+public class SliderPanel extends Panel\r
{\r
AlignmentPanel ap;\r
boolean forConservation = true;\r
public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,\r
ColourSchemeI cs)\r
{\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
this.ap = ap;\r
this.cs = cs;\r
forConservation = forConserve;\r
return Integer.parseInt(valueField.getText());\r
}\r
\r
+ // this is used for conservation colours, PID colours and redundancy threshold\r
+ protected Scrollbar slider = new Scrollbar();\r
+ protected TextField valueField = new TextField();\r
+ protected Label label = new Label();\r
+ Panel jPanel1 = new Panel();\r
+ Panel jPanel2 = new Panel();\r
+ protected Button applyButton = new Button();\r
+ protected Button undoButton = new Button();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ protected Checkbox allGroupsCheck = new Checkbox();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+ FlowLayout flowLayout2 = new FlowLayout();\r
+\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(borderLayout2);\r
+\r
+ // slider.setMajorTickSpacing(10);\r
+ // slider.setMinorTickSpacing(1);\r
+ // slider.setPaintTicks(true);\r
+ slider.setBackground(Color.white);\r
+ slider.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ slider.setOrientation(0);\r
+ valueField.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ valueField.setText(" ");\r
+ valueField.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ valueField_actionPerformed(e);\r
+ }\r
+ });\r
+ label.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ label.setText("set this label text");\r
+ jPanel1.setLayout(borderLayout1);\r
+ jPanel2.setLayout(flowLayout1);\r
+ applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ applyButton.setLabel("Apply");\r
+ applyButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ applyButton_actionPerformed(e);\r
+ }\r
+ });\r
+ undoButton.setEnabled(false);\r
+ undoButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ undoButton.setLabel("Undo");\r
+ undoButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ undoButton_actionPerformed(e);\r
+ }\r
+ });\r
+ allGroupsCheck.setEnabled(false);\r
+ allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ allGroupsCheck.setLabel("Apply threshold to all groups");\r
+ allGroupsCheck.setName("Apply to all Groups");\r
+ this.setBackground(Color.white);\r
+ this.setForeground(Color.black);\r
+ jPanel2.add(label, null);\r
+ jPanel2.add(applyButton, null);\r
+ jPanel2.add(undoButton, null);\r
+ jPanel2.add(allGroupsCheck);\r
+ jPanel1.add(valueField, java.awt.BorderLayout.EAST);\r
+ jPanel1.add(slider, java.awt.BorderLayout.CENTER);\r
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
+ this.add(jPanel2, java.awt.BorderLayout.CENTER);\r
+ }\r
+\r
+ protected void applyButton_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void undoButton_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
}\r
\r
g.setFont(font);\r
\r
+\r
FontMetrics fm = g.getFontMetrics(font);\r
\r
if (nameHash.size() == 0)\r
import java.util.*;\r
\r
import java.awt.event.*;\r
+import java.awt.*;\r
\r
import jalview.analysis.*;\r
import jalview.datamodel.*;\r
import jalview.io.*;\r
-import jalview.jbappletgui.*;\r
\r
-public class TreePanel\r
- extends GTreePanel\r
+public class TreePanel extends Frame\r
{\r
SequenceI[] seq;\r
String type;\r
String pwtype;\r
- AlignmentPanel ap;\r
int start;\r
int end;\r
TreeCanvas treeCanvas;\r
public TreePanel(AlignViewport av, Vector seqVector, String type,\r
String pwtype, int s, int e)\r
{\r
- super();\r
+ try\r
+ {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
}\r
\r
public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
String type, String pwtype)\r
{\r
- super();\r
+ try\r
+ {\r
+ jbInit();\r
+ this.setMenuBar(jMenuBar1);\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
}\r
\r
{\r
jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
String output = fout.print(false, true);\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);\r
cap.setText(output);\r
java.awt.Frame frame = new java.awt.Frame();\r
frame.add(cap);\r
treeCanvas.setMarkPlaceholders(placeholdersMenu.getState());\r
}\r
\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ protected ScrollPane scrollPane = new ScrollPane();\r
+ MenuBar jMenuBar1 = new MenuBar();\r
+ Menu jMenu2 = new Menu();\r
+ protected MenuItem fontSize = new MenuItem();\r
+ protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
+ Menu fileMenu = new Menu();\r
+ MenuItem newickOutput = new MenuItem();\r
+\r
+ private void jbInit() throws Exception {\r
+ setLayout(borderLayout1);\r
+ this.setBackground(Color.white);\r
+ this.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jMenu2.setLabel("View");\r
+ fontSize.setLabel("Font...");\r
+ fontSize.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ fontSize_actionPerformed(e);\r
+ }\r
+ });\r
+ bootstrapMenu.setLabel("Show Bootstrap Values");\r
+ bootstrapMenu.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ bootstrapMenu_actionPerformed(null);\r
+ }\r
+ });\r
+ distanceMenu.setLabel("Show Distances");\r
+ distanceMenu.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ distanceMenu_actionPerformed(null);\r
+ }\r
+ });\r
+ placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
+ placeholdersMenu.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ placeholdersMenu_actionPerformed(null);\r
+ }\r
+ });\r
+ fitToWindow.setState(true);\r
+ fitToWindow.setLabel("Fit To Window");\r
+ fitToWindow.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ fitToWindow_actionPerformed(null);\r
+ }\r
+ });\r
+ fileMenu.setLabel("File");\r
+ newickOutput.setLabel("Newick Format");\r
+ newickOutput.addActionListener(new ActionListener() {\r
+ public void actionPerformed(ActionEvent actionEvent) {\r
+ newickOutput_actionPerformed(actionEvent);\r
+ }\r
+ });\r
+\r
+ add(scrollPane, BorderLayout.CENTER);\r
+ jMenuBar1.add(fileMenu);\r
+ jMenuBar1.add(jMenu2);\r
+ jMenu2.add(fitToWindow);\r
+ jMenu2.add(fontSize);\r
+ jMenu2.add(distanceMenu);\r
+ jMenu2.add(bootstrapMenu);\r
+ jMenu2.add(placeholdersMenu);\r
+ fileMenu.add(newickOutput);\r
+ }\r
+\r
}\r
import java.awt.event.*;\r
\r
import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
import jalview.schemes.*;\r
\r
public class UserDefinedColours\r
- extends GUserDefinedColours\r
+ extends Panel\r
{\r
\r
AlignmentPanel ap;\r
\r
public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)\r
{\r
- super();\r
+ try {\r
+ jbInit();\r
+ } catch (Exception e) {\r
+ e.printStackTrace();\r
+ }\r
frame = new Frame();\r
frame.add(this);\r
jalview.bin.JalviewLite.addFrame(frame, "User defined colours", 420, 345);\r
frame.setVisible(false);\r
}\r
\r
+\r
+ protected Panel buttonPanel = new Panel();\r
+ protected GridLayout gridLayout = new GridLayout();\r
+ Panel jPanel2 = new Panel();\r
+ protected Button okButton = new Button();\r
+ protected Button applyButton = new Button();\r
+ protected Button cancelButton = new Button();\r
+ protected Scrollbar rScroller = new Scrollbar();\r
+ Label label1 = new Label();\r
+ protected TextField rText = new TextField();\r
+ Label label4 = new Label();\r
+ protected Scrollbar gScroller = new Scrollbar();\r
+ protected TextField gText = new TextField();\r
+ Label label5 = new Label();\r
+ protected Scrollbar bScroller = new Scrollbar();\r
+ protected TextField bText = new TextField();\r
+ protected Panel target = new Panel();\r
+\r
+ private void jbInit() throws Exception {\r
+ this.setLayout(null);\r
+ buttonPanel.setLayout(gridLayout);\r
+ gridLayout.setColumns(6);\r
+ gridLayout.setRows(4);\r
+ okButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ okButton.setLabel("OK");\r
+ okButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ okButton_actionPerformed(e);\r
+ }\r
+ });\r
+ applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ applyButton.setLabel("Apply");\r
+ applyButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ applyButton_actionPerformed(e);\r
+ }\r
+ });\r
+ cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ cancelButton.setLabel("Cancel");\r
+ cancelButton.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ cancelButton_actionPerformed(e);\r
+ }\r
+ });\r
+ this.setBackground(new Color(212, 208, 223));\r
+ jPanel2.setBounds(new Rectangle(0, 265, 400, 35));\r
+ buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));\r
+ rScroller.setMaximum(256);\r
+ rScroller.setMinimum(0);\r
+ rScroller.setOrientation(0);\r
+ rScroller.setUnitIncrement(1);\r
+ rScroller.setVisibleAmount(1);\r
+ rScroller.setBounds(new Rectangle(36, 27, 119, 19));\r
+ rScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
+ public void adjustmentValueChanged(AdjustmentEvent e) {\r
+ rScroller_adjustmentValueChanged(e);\r
+ }\r
+ });\r
+ label1.setAlignment(Label.RIGHT);\r
+ label1.setText("R");\r
+ label1.setBounds(new Rectangle(19, 30, 16, 15));\r
+ rText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));\r
+ rText.setText("0 ");\r
+ rText.setBounds(new Rectangle(156, 27, 53, 19));\r
+ rText.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ rText_actionPerformed(e);\r
+ }\r
+ });\r
+ label4.setAlignment(Label.RIGHT);\r
+ label4.setText("G");\r
+ label4.setBounds(new Rectangle(15, 56, 20, 15));\r
+ gScroller.setMaximum(256);\r
+ gScroller.setMinimum(0);\r
+ gScroller.setOrientation(0);\r
+ gScroller.setUnitIncrement(1);\r
+ gScroller.setVisibleAmount(1);\r
+ gScroller.setBounds(new Rectangle(35, 52, 120, 20));\r
+ gScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
+ public void adjustmentValueChanged(AdjustmentEvent e) {\r
+ gScroller_adjustmentValueChanged(e);\r
+ }\r
+ });\r
+ gText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));\r
+ gText.setText("0 ");\r
+ gText.setBounds(new Rectangle(156, 52, 53, 20));\r
+ gText.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ gText_actionPerformed(e);\r
+ }\r
+ });\r
+ label5.setAlignment(Label.RIGHT);\r
+ label5.setText("B");\r
+ label5.setBounds(new Rectangle(14, 82, 20, 15));\r
+ bScroller.setMaximum(256);\r
+ bScroller.setMinimum(0);\r
+ bScroller.setOrientation(0);\r
+ bScroller.setUnitIncrement(1);\r
+ bScroller.setVisibleAmount(1);\r
+ bScroller.setBounds(new Rectangle(35, 78, 120, 20));\r
+ bScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
+ public void adjustmentValueChanged(AdjustmentEvent e) {\r
+ bScroller_adjustmentValueChanged(e);\r
+ }\r
+ });\r
+ bText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));\r
+ bText.setText("0 ");\r
+ bText.setBounds(new Rectangle(157, 78, 52, 20));\r
+ bText.addActionListener(new java.awt.event.ActionListener() {\r
+ public void actionPerformed(ActionEvent e) {\r
+ bText_actionPerformed(e);\r
+ }\r
+ });\r
+ target.setBackground(Color.black);\r
+ target.setBounds(new Rectangle(229, 26, 134, 79));\r
+ this.add(jPanel2, null);\r
+ jPanel2.add(okButton, null);\r
+ jPanel2.add(applyButton, null);\r
+ jPanel2.add(cancelButton, null);\r
+ this.add(buttonPanel, null);\r
+ this.add(target, null);\r
+ this.add(gScroller);\r
+ this.add(rScroller);\r
+ this.add(bScroller);\r
+ this.add(label5);\r
+ this.add(label4);\r
+ this.add(label1);\r
+ this.add(gText);\r
+ this.add(rText);\r
+ this.add(bText);\r
+}\r
+\r
}\r
System.out.println("Usage: jalview -open [FILE] [OUTPUT_FORMAT] [OUTPUT_FILE]\n\n"\r
+"-nodisplay\tRun Jalview without User Interface.\n"\r
+"-props FILE\tUse the given Jalview properties file instead of users default.\n"\r
- +"-groups FILE\tUse the given file to mark groups on the alignment. \nGroups file is in the following tab delimited format\n"\r
- +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>COLOUR\n"\r
+ +"-groups FILE\tUse the given file to mark groups on the alignment."\r
+ +"\nThe first lines of the groups file lists the GroupName and GroupColours"\r
+ +" to be used in the alignment. Use the GROUPNAME label for each of your sequences. "\r
+ +"\nGROUPNAME<tab>GROUPCOLOUR\n"\r
+ +"TEXT<tab>SEQUENCE_ID<tab>SEQUENCE_INDEX<tab>START_RESIDUE<tab>END_RESIDUE<tab>GROUPNAME\n"\r
+"SequenceID is used in preference to SequenceIndex if both are provided.\n"\r
+"Enter ID_NOT_SPECIFIED for SEQUENCE_ID or -1 for SEQUENCE_INDEX if unknown.\n"\r
+"COLOUR can be hexadecimal RGB or 'red', 'blue' etc.\n\n"\r
{\r
static int lastFrameX = 200;\r
static int lastFrameY = 200;\r
- static Applet applet;\r
boolean fileFound = true;\r
String file = "No file";\r
Button launcher = new Button("Start Jalview");\r
\r
+ AlignFrame currentAlignFrame;\r
+\r
+\r
/**\r
* init method for Jalview Applet\r
*/\r
public void init()\r
{\r
- applet = this;\r
-\r
int r = 255;\r
int g = 255;\r
int b = 255;\r
}\r
}\r
\r
+ param = getParameter("label");\r
+ if(param != null)\r
+ launcher.setLabel(param);\r
+\r
this.setBackground(new Color(r, g, b));\r
\r
- file = getParameter("file");\r
\r
+ param = getParameter("features");\r
+ if(param!=null)\r
+ {\r
+ if(param.indexOf("://")==-1)\r
+ param = getCodeBase() + param;\r
+ }\r
+ final String featuresFile = param;\r
+\r
+ file = getParameter("file");\r
+ final JalviewLite applet = this;\r
if (file != null)\r
{\r
add(launcher);\r
- file = applet.getCodeBase() + file;\r
+ if(file.indexOf("://")==-1)\r
+ file = getCodeBase() + file;\r
+\r
launcher.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
String format = jalview.io.IdentifyFile.Identify(file,\r
"URL");\r
- LoadFile(file, "URL", format);\r
- }\r
+ LoadingThread loader = new LoadingThread(file,\r
+ "URL",\r
+ format,\r
+ featuresFile,\r
+ applet);\r
+ loader.start();\r
+ }\r
});\r
}\r
else\r
}\r
}\r
\r
+\r
public static void main(String [] args)\r
{\r
if(args.length!=1)\r
System.exit(1);\r
}\r
\r
-\r
String format = jalview.io.IdentifyFile.Identify(args[0],"File");\r
- SequenceI[] sequences = new FormatAdapter().readFile(args[0], "File", format);\r
+ SequenceI[] sequences = new AppletFormatAdapter().readFile(args[0], "File", format);\r
\r
if ( (sequences != null) && (sequences.length > 0))\r
{\r
}\r
}\r
\r
- /**\r
- * Displays the given URL in a new browser window\r
- *\r
- * @param url URL to display in browser window.\r
- * <br>New window will be named "HELP_WINDOW"\r
- */\r
- public static void showURL(String url)\r
- {\r
- showURL(url, "HELP");\r
- }\r
-\r
- public static void showURL(String url, String target)\r
- {\r
- if(applet==null)\r
- {\r
- System.out.println("Not running as applet - no browser available.");\r
- }\r
- else\r
- {\r
- try\r
- {\r
- applet.getAppletContext().showDocument(new java.net.URL(url),\r
- target);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
-\r
- /**\r
- * Starts a new LoadingThread for loading an alignment file\r
- *\r
- * @param file file name including full path to file\r
- * @param protocol file or URL or paste\r
- * @param format Fasta, Clustal, PFAM, MSF, PIR, BLC, Jalview\r
- */\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- LoadingThread loader = new LoadingThread(file, protocol, format, this);\r
- loader.start();\r
- }\r
\r
/**\r
* Initialises and displays a new java.awt.Frame\r
{\r
public void windowClosing(WindowEvent e)\r
{\r
+ lastFrameX -=40;\r
+ lastFrameY-=40;\r
frame.dispose();\r
}\r
});\r
frame.setVisible(true);\r
}\r
\r
+ public String getAlignment(String format)\r
+ {\r
+ return getAlignment(format, "true");\r
+ }\r
+\r
+ public String getAlignment(String format, String suffix)\r
+ {\r
+ try\r
+ {\r
+ boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+\r
+ String reply = new AppletFormatAdapter().formatSequences(format,\r
+ currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);\r
+ return reply;\r
+ }\r
+ catch (Exception ex)\r
+ {ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+\r
+ }\r
+ }\r
+\r
/**\r
* This paints the background surrounding the "Launch Jalview button"\r
* <br>\r
String file;\r
String protocol;\r
String format;\r
- JalviewLite jlapplet;\r
+ String featuresFile;\r
+ JalviewLite applet;\r
\r
- public LoadingThread(String file, String protocol, String format,\r
- JalviewLite applet)\r
+ public LoadingThread(String file,\r
+ String protocol,\r
+ String format,\r
+ String features,\r
+ JalviewLite applet)\r
{\r
this.file = file;\r
this.protocol = protocol;\r
this.format = format;\r
- this.jlapplet = applet;\r
+ featuresFile = features;\r
+ this.applet = applet;\r
}\r
\r
public void run()\r
{\r
SequenceI[] sequences = null;\r
- sequences = new FormatAdapter().readFile(file, protocol, format);\r
+ sequences = new AppletFormatAdapter().readFile(file, protocol, format);\r
\r
if ((sequences != null) && (sequences.length > 0))\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences),\r
- jlapplet, file);\r
- af.statusBar.setText("Successfully loaded file " + file);\r
+ currentAlignFrame = new AlignFrame(new Alignment(sequences),\r
+ applet, file);\r
+ currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
+\r
+ if(featuresFile!=null)\r
+ currentAlignFrame.parseFeaturesFile(featuresFile);\r
+\r
+ String pdbfile = applet.getParameter("PDBFILE");\r
+ if(pdbfile!=null)\r
+ {\r
+ if(pdbfile.indexOf("://")==-1)\r
+ pdbfile = getCodeBase() + pdbfile;\r
+\r
+ String sequence = applet.getParameter("PDBSEQ");\r
+\r
+ if(sequence!=null)\r
+ {\r
+ new MCview.AppletPDBViewer(pdbfile, "URL",\r
+ (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence),\r
+ currentAlignFrame.getSeqcanvas());\r
+\r
+\r
+ }\r
+\r
+ }\r
}\r
else\r
{\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class Feature.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Feature implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _begin\r
+ */\r
+ private int _begin;\r
+\r
+ /**\r
+ * keeps track of state for field: _begin\r
+ */\r
+ private boolean _has_begin;\r
+\r
+ /**\r
+ * Field _end\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+ /**\r
+ * Field _type\r
+ */\r
+ private java.lang.String _type;\r
+\r
+ /**\r
+ * Field _description\r
+ */\r
+ private java.lang.String _description;\r
+\r
+ /**\r
+ * Field _status\r
+ */\r
+ private java.lang.String _status;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Feature() {\r
+ super();\r
+ } //-- jalview.binding.Feature()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method deleteBegin\r
+ * \r
+ */\r
+ public void deleteBegin()\r
+ {\r
+ this._has_begin= false;\r
+ } //-- void deleteBegin() \r
+\r
+ /**\r
+ * Method deleteEnd\r
+ * \r
+ */\r
+ public void deleteEnd()\r
+ {\r
+ this._has_end= false;\r
+ } //-- void deleteEnd() \r
+\r
+ /**\r
+ * Returns the value of field 'begin'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'begin'.\r
+ */\r
+ public int getBegin()\r
+ {\r
+ return this._begin;\r
+ } //-- int getBegin() \r
+\r
+ /**\r
+ * Returns the value of field 'description'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'description'.\r
+ */\r
+ public java.lang.String getDescription()\r
+ {\r
+ return this._description;\r
+ } //-- java.lang.String getDescription() \r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'end'.\r
+ */\r
+ public int getEnd()\r
+ {\r
+ return this._end;\r
+ } //-- int getEnd() \r
+\r
+ /**\r
+ * Returns the value of field 'status'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'status'.\r
+ */\r
+ public java.lang.String getStatus()\r
+ {\r
+ return this._status;\r
+ } //-- java.lang.String getStatus() \r
+\r
+ /**\r
+ * Returns the value of field 'type'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'type'.\r
+ */\r
+ public java.lang.String getType()\r
+ {\r
+ return this._type;\r
+ } //-- java.lang.String getType() \r
+\r
+ /**\r
+ * Method hasBegin\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasBegin()\r
+ {\r
+ return this._has_begin;\r
+ } //-- boolean hasBegin() \r
+\r
+ /**\r
+ * Method hasEnd\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasEnd()\r
+ {\r
+ return this._has_end;\r
+ } //-- boolean hasEnd() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Sets the value of field 'begin'.\r
+ * \r
+ * @param begin the value of field 'begin'.\r
+ */\r
+ public void setBegin(int begin)\r
+ {\r
+ this._begin = begin;\r
+ this._has_begin = true;\r
+ } //-- void setBegin(int) \r
+\r
+ /**\r
+ * Sets the value of field 'description'.\r
+ * \r
+ * @param description the value of field 'description'.\r
+ */\r
+ public void setDescription(java.lang.String description)\r
+ {\r
+ this._description = description;\r
+ } //-- void setDescription(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(int end)\r
+ {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ } //-- void setEnd(int) \r
+\r
+ /**\r
+ * Sets the value of field 'status'.\r
+ * \r
+ * @param status the value of field 'status'.\r
+ */\r
+ public void setStatus(java.lang.String status)\r
+ {\r
+ this._status = status;\r
+ } //-- void setStatus(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'type'.\r
+ * \r
+ * @param type the value of field 'type'.\r
+ */\r
+ public void setType(java.lang.String type)\r
+ {\r
+ this._type = type;\r
+ } //-- void setType(java.lang.String) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class FeatureSettings.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class FeatureSettings implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _settingList\r
+ */\r
+ private java.util.Vector _settingList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public FeatureSettings() {\r
+ super();\r
+ _settingList = new Vector();\r
+ } //-- jalview.binding.FeatureSettings()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addSetting\r
+ * \r
+ * \r
+ * \r
+ * @param vSetting\r
+ */\r
+ public void addSetting(jalview.binding.Setting vSetting)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _settingList.addElement(vSetting);\r
+ } //-- void addSetting(jalview.binding.Setting) \r
+\r
+ /**\r
+ * Method addSetting\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSetting\r
+ */\r
+ public void addSetting(int index, jalview.binding.Setting vSetting)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _settingList.insertElementAt(vSetting, index);\r
+ } //-- void addSetting(int, jalview.binding.Setting) \r
+\r
+ /**\r
+ * Method enumerateSetting\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateSetting()\r
+ {\r
+ return _settingList.elements();\r
+ } //-- java.util.Enumeration enumerateSetting() \r
+\r
+ /**\r
+ * Method getSetting\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Setting\r
+ */\r
+ public jalview.binding.Setting getSetting(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _settingList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.Setting) _settingList.elementAt(index);\r
+ } //-- jalview.binding.Setting getSetting(int) \r
+\r
+ /**\r
+ * Method getSetting\r
+ * \r
+ * \r
+ * \r
+ * @return Setting\r
+ */\r
+ public jalview.binding.Setting[] getSetting()\r
+ {\r
+ int size = _settingList.size();\r
+ jalview.binding.Setting[] mArray = new jalview.binding.Setting[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Setting) _settingList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.Setting[] getSetting() \r
+\r
+ /**\r
+ * Method getSettingCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getSettingCount()\r
+ {\r
+ return _settingList.size();\r
+ } //-- int getSettingCount() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method removeAllSetting\r
+ * \r
+ */\r
+ public void removeAllSetting()\r
+ {\r
+ _settingList.removeAllElements();\r
+ } //-- void removeAllSetting() \r
+\r
+ /**\r
+ * Method removeSetting\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Setting\r
+ */\r
+ public jalview.binding.Setting removeSetting(int index)\r
+ {\r
+ java.lang.Object obj = _settingList.elementAt(index);\r
+ _settingList.removeElementAt(index);\r
+ return (jalview.binding.Setting) obj;\r
+ } //-- jalview.binding.Setting removeSetting(int) \r
+\r
+ /**\r
+ * Method setSetting\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSetting\r
+ */\r
+ public void setSetting(int index, jalview.binding.Setting vSetting)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _settingList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _settingList.setElementAt(vSetting, index);\r
+ } //-- void setSetting(int, jalview.binding.Setting) \r
+\r
+ /**\r
+ * Method setSetting\r
+ * \r
+ * \r
+ * \r
+ * @param settingArray\r
+ */\r
+ public void setSetting(jalview.binding.Setting[] settingArray)\r
+ {\r
+ //-- copy array\r
+ _settingList.removeAllElements();\r
+ for (int i = 0; i < settingArray.length; i++) {\r
+ _settingList.addElement(settingArray[i]);\r
+ }\r
+ } //-- void setSetting(jalview.binding.Setting) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class Features.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Features extends Feature \r
+implements java.io.Serializable\r
+{\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Features() {\r
+ super();\r
+ } //-- jalview.binding.Features()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Features) Unmarshaller.unmarshal(jalview.binding.Features.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
*/\r
private boolean _has_id;\r
\r
+ /**\r
+ * Field _featuresList\r
+ */\r
+ private java.util.Vector _featuresList;\r
+\r
+ /**\r
+ * Field _pdbidsList\r
+ */\r
+ private java.util.Vector _pdbidsList;\r
+\r
\r
//----------------/\r
//- Constructors -/\r
\r
public JSeq() {\r
super();\r
+ _featuresList = new Vector();\r
+ _pdbidsList = new Vector();\r
} //-- jalview.binding.JSeq()\r
\r
\r
//-----------/\r
\r
/**\r
+ * Method addFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param vFeatures\r
+ */\r
+ public void addFeatures(jalview.binding.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _featuresList.addElement(vFeatures);\r
+ } //-- void addFeatures(jalview.binding.Features) \r
+\r
+ /**\r
+ * Method addFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vFeatures\r
+ */\r
+ public void addFeatures(int index, jalview.binding.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _featuresList.insertElementAt(vFeatures, index);\r
+ } //-- void addFeatures(int, jalview.binding.Features) \r
+\r
+ /**\r
+ * Method addPdbids\r
+ * \r
+ * \r
+ * \r
+ * @param vPdbids\r
+ */\r
+ public void addPdbids(jalview.binding.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _pdbidsList.addElement(vPdbids);\r
+ } //-- void addPdbids(jalview.binding.Pdbids) \r
+\r
+ /**\r
+ * Method addPdbids\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbids\r
+ */\r
+ public void addPdbids(int index, jalview.binding.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _pdbidsList.insertElementAt(vPdbids, index);\r
+ } //-- void addPdbids(int, jalview.binding.Pdbids) \r
+\r
+ /**\r
* Method deleteColour\r
* \r
*/\r
} //-- void deleteStart() \r
\r
/**\r
+ * Method enumerateFeatures\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateFeatures()\r
+ {\r
+ return _featuresList.elements();\r
+ } //-- java.util.Enumeration enumerateFeatures() \r
+\r
+ /**\r
+ * Method enumeratePdbids\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumeratePdbids()\r
+ {\r
+ return _pdbidsList.elements();\r
+ } //-- java.util.Enumeration enumeratePdbids() \r
+\r
+ /**\r
* Returns the value of field 'colour'.\r
* \r
* @return int\r
} //-- int getEnd() \r
\r
/**\r
+ * Method getFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Features\r
+ */\r
+ public jalview.binding.Features getFeatures(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _featuresList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.Features) _featuresList.elementAt(index);\r
+ } //-- jalview.binding.Features getFeatures(int) \r
+\r
+ /**\r
+ * Method getFeatures\r
+ * \r
+ * \r
+ * \r
+ * @return Features\r
+ */\r
+ public jalview.binding.Features[] getFeatures()\r
+ {\r
+ int size = _featuresList.size();\r
+ jalview.binding.Features[] mArray = new jalview.binding.Features[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Features) _featuresList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.Features[] getFeatures() \r
+\r
+ /**\r
+ * Method getFeaturesCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getFeaturesCount()\r
+ {\r
+ return _featuresList.size();\r
+ } //-- int getFeaturesCount() \r
+\r
+ /**\r
* Returns the value of field 'id'.\r
* \r
* @return int\r
} //-- int getId() \r
\r
/**\r
+ * Method getPdbids\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Pdbids\r
+ */\r
+ public jalview.binding.Pdbids getPdbids(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _pdbidsList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.Pdbids) _pdbidsList.elementAt(index);\r
+ } //-- jalview.binding.Pdbids getPdbids(int) \r
+\r
+ /**\r
+ * Method getPdbids\r
+ * \r
+ * \r
+ * \r
+ * @return Pdbids\r
+ */\r
+ public jalview.binding.Pdbids[] getPdbids()\r
+ {\r
+ int size = _pdbidsList.size();\r
+ jalview.binding.Pdbids[] mArray = new jalview.binding.Pdbids[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Pdbids) _pdbidsList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.Pdbids[] getPdbids() \r
+\r
+ /**\r
+ * Method getPdbidsCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getPdbidsCount()\r
+ {\r
+ return _pdbidsList.size();\r
+ } //-- int getPdbidsCount() \r
+\r
+ /**\r
* Returns the value of field 'start'.\r
* \r
* @return int\r
} //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
+ * Method removeAllFeatures\r
+ * \r
+ */\r
+ public void removeAllFeatures()\r
+ {\r
+ _featuresList.removeAllElements();\r
+ } //-- void removeAllFeatures() \r
+\r
+ /**\r
+ * Method removeAllPdbids\r
+ * \r
+ */\r
+ public void removeAllPdbids()\r
+ {\r
+ _pdbidsList.removeAllElements();\r
+ } //-- void removeAllPdbids() \r
+\r
+ /**\r
+ * Method removeFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Features\r
+ */\r
+ public jalview.binding.Features removeFeatures(int index)\r
+ {\r
+ java.lang.Object obj = _featuresList.elementAt(index);\r
+ _featuresList.removeElementAt(index);\r
+ return (jalview.binding.Features) obj;\r
+ } //-- jalview.binding.Features removeFeatures(int) \r
+\r
+ /**\r
+ * Method removePdbids\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Pdbids\r
+ */\r
+ public jalview.binding.Pdbids removePdbids(int index)\r
+ {\r
+ java.lang.Object obj = _pdbidsList.elementAt(index);\r
+ _pdbidsList.removeElementAt(index);\r
+ return (jalview.binding.Pdbids) obj;\r
+ } //-- jalview.binding.Pdbids removePdbids(int) \r
+\r
+ /**\r
* Sets the value of field 'colour'.\r
* \r
* @param colour the value of field 'colour'.\r
} //-- void setEnd(int) \r
\r
/**\r
+ * Method setFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vFeatures\r
+ */\r
+ public void setFeatures(int index, jalview.binding.Features vFeatures)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _featuresList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _featuresList.setElementAt(vFeatures, index);\r
+ } //-- void setFeatures(int, jalview.binding.Features) \r
+\r
+ /**\r
+ * Method setFeatures\r
+ * \r
+ * \r
+ * \r
+ * @param featuresArray\r
+ */\r
+ public void setFeatures(jalview.binding.Features[] featuresArray)\r
+ {\r
+ //-- copy array\r
+ _featuresList.removeAllElements();\r
+ for (int i = 0; i < featuresArray.length; i++) {\r
+ _featuresList.addElement(featuresArray[i]);\r
+ }\r
+ } //-- void setFeatures(jalview.binding.Features) \r
+\r
+ /**\r
* Sets the value of field 'id'.\r
* \r
* @param id the value of field 'id'.\r
} //-- void setId(int) \r
\r
/**\r
+ * Method setPdbids\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbids\r
+ */\r
+ public void setPdbids(int index, jalview.binding.Pdbids vPdbids)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _pdbidsList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _pdbidsList.setElementAt(vPdbids, index);\r
+ } //-- void setPdbids(int, jalview.binding.Pdbids) \r
+\r
+ /**\r
+ * Method setPdbids\r
+ * \r
+ * \r
+ * \r
+ * @param pdbidsArray\r
+ */\r
+ public void setPdbids(jalview.binding.Pdbids[] pdbidsArray)\r
+ {\r
+ //-- copy array\r
+ _pdbidsList.removeAllElements();\r
+ for (int i = 0; i < pdbidsArray.length; i++) {\r
+ _pdbidsList.addElement(pdbidsArray[i]);\r
+ }\r
+ } //-- void setPdbids(jalview.binding.Pdbids) \r
+\r
+ /**\r
* Sets the value of field 'start'.\r
* \r
* @param start the value of field 'start'.\r
*/\r
private java.util.Vector _treeList;\r
\r
+ /**\r
+ * Field _featureSettings\r
+ */\r
+ private jalview.binding.FeatureSettings _featureSettings;\r
+\r
\r
//----------------/\r
//- Constructors -/\r
} //-- java.util.Enumeration enumerateViewport() \r
\r
/**\r
+ * Returns the value of field 'featureSettings'.\r
+ * \r
+ * @return FeatureSettings\r
+ * @return the value of field 'featureSettings'.\r
+ */\r
+ public jalview.binding.FeatureSettings getFeatureSettings()\r
+ {\r
+ return this._featureSettings;\r
+ } //-- jalview.binding.FeatureSettings getFeatureSettings() \r
+\r
+ /**\r
* Method getJGroup\r
* \r
* \r
} //-- jalview.binding.Viewport removeViewport(int) \r
\r
/**\r
+ * Sets the value of field 'featureSettings'.\r
+ * \r
+ * @param featureSettings the value of field 'featureSettings'.\r
+ */\r
+ public void setFeatureSettings(jalview.binding.FeatureSettings featureSettings)\r
+ {\r
+ this._featureSettings = featureSettings;\r
+ } //-- void setFeatureSettings(jalview.binding.FeatureSettings) \r
+\r
+ /**\r
* Method setJGroup\r
* \r
* \r
+++ /dev/null
-/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-package jalview.binding;\r
-\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-\r
-import org.xml.sax.ContentHandler;\r
-\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-\r
-\r
-/**\r
- * Class JalviewModelSequence2.\r
- *\r
- * @version $Revision$ $Date$\r
- */\r
-public class JalviewModelSequence2 implements java.io.Serializable\r
-{\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _items\r
- */\r
- private java.util.Vector _items;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
- public JalviewModelSequence2()\r
- {\r
- super();\r
- _items = new Vector();\r
- }\r
-\r
- //-- jalview.binding.JalviewModelSequence2()\r
- //-----------/\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param vJalviewModelSequence2Item DOCUMENT ME!\r
- *\r
- * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME!\r
- */\r
- public void addJalviewModelSequence2Item(\r
- jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _items.addElement(vJalviewModelSequence2Item);\r
- }\r
-\r
- //-- void addJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) \r
-\r
- /**\r
- * Method addJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vJalviewModelSequence2Item\r
- */\r
- public void addJalviewModelSequence2Item(int index,\r
- jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _items.insertElementAt(vJalviewModelSequence2Item, index);\r
- }\r
-\r
- //-- void addJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) \r
-\r
- /**\r
- * Method enumerateJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateJalviewModelSequence2Item()\r
- {\r
- return _items.elements();\r
- }\r
-\r
- //-- java.util.Enumeration enumerateJalviewModelSequence2Item() \r
-\r
- /**\r
- * Method getJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return JalviewModelSequence2Item\r
- */\r
- public jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(\r
- int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _items.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);\r
- }\r
-\r
- //-- jalview.binding.JalviewModelSequence2Item getJalviewModelSequence2Item(int) \r
-\r
- /**\r
- * Method getJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
- * @return JalviewModelSequence2Item\r
- */\r
- public jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item()\r
- {\r
- int size = _items.size();\r
- jalview.binding.JalviewModelSequence2Item[] mArray = new jalview.binding.JalviewModelSequence2Item[size];\r
-\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.JalviewModelSequence2Item) _items.elementAt(index);\r
- }\r
-\r
- return mArray;\r
- }\r
-\r
- //-- jalview.binding.JalviewModelSequence2Item[] getJalviewModelSequence2Item() \r
-\r
- /**\r
- * Method getJalviewModelSequence2ItemCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getJalviewModelSequence2ItemCount()\r
- {\r
- return _items.size();\r
- }\r
-\r
- //-- int getJalviewModelSequence2ItemCount() \r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
-\r
- return true;\r
- }\r
-\r
- //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, \r
- org.exolab.castor.xml.ValidationException\r
- {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, \r
- org.exolab.castor.xml.ValidationException\r
- {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Method removeAllJalviewModelSequence2Item\r
- *\r
- */\r
- public void removeAllJalviewModelSequence2Item()\r
- {\r
- _items.removeAllElements();\r
- }\r
-\r
- //-- void removeAllJalviewModelSequence2Item() \r
-\r
- /**\r
- * Method removeJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return JalviewModelSequence2Item\r
- */\r
- public jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(\r
- int index)\r
- {\r
- java.lang.Object obj = _items.elementAt(index);\r
- _items.removeElementAt(index);\r
-\r
- return (jalview.binding.JalviewModelSequence2Item) obj;\r
- }\r
-\r
- //-- jalview.binding.JalviewModelSequence2Item removeJalviewModelSequence2Item(int) \r
-\r
- /**\r
- * Method setJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vJalviewModelSequence2Item\r
- */\r
- public void setJalviewModelSequence2Item(int index,\r
- jalview.binding.JalviewModelSequence2Item vJalviewModelSequence2Item)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _items.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- _items.setElementAt(vJalviewModelSequence2Item, index);\r
- }\r
-\r
- //-- void setJalviewModelSequence2Item(int, jalview.binding.JalviewModelSequence2Item) \r
-\r
- /**\r
- * Method setJalviewModelSequence2Item\r
- *\r
- *\r
- *\r
- * @param jalviewModelSequence2ItemArray\r
- */\r
- public void setJalviewModelSequence2Item(\r
- jalview.binding.JalviewModelSequence2Item[] jalviewModelSequence2ItemArray)\r
- {\r
- //-- copy array\r
- _items.removeAllElements();\r
-\r
- for (int i = 0; i < jalviewModelSequence2ItemArray.length; i++)\r
- {\r
- _items.addElement(jalviewModelSequence2ItemArray[i]);\r
- }\r
- }\r
-\r
- //-- void setJalviewModelSequence2Item(jalview.binding.JalviewModelSequence2Item) \r
-\r
- /**\r
- * Method unmarshal\r
- *\r
- *\r
- *\r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, \r
- org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.binding.JalviewModelSequence2) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence2.class,\r
- reader);\r
- }\r
-\r
- //-- java.lang.Object unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- *\r
- */\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- }\r
-\r
- //-- void validate() \r
-}\r
+++ /dev/null
-/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.binding;\r
-\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
-\r
-/**\r
- * Class JalviewModelSequence2Item.\r
- *\r
- * @version $Revision$ $Date$\r
- */\r
-public class JalviewModelSequence2Item\r
- implements java.io.Serializable\r
-{\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _userColourSchemeList\r
- */\r
- private java.util.Vector _userColourSchemeList;\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JalviewModelSequence2Item()\r
- {\r
- super();\r
- _userColourSchemeList = new Vector();\r
- } //-- jalview.binding.JalviewModelSequence2Item()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addUserColourScheme\r
- *\r
- *\r
- *\r
- * @param vUserColourScheme\r
- */\r
- public void addUserColourScheme(jalview.binding.UserColourScheme\r
- vUserColourScheme)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColourSchemeList.addElement(vUserColourScheme);\r
- } //-- void addUserColourScheme(jalview.binding.UserColourScheme)\r
-\r
- /**\r
- * Method addUserColourScheme\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vUserColourScheme\r
- */\r
- public void addUserColourScheme(int index,\r
- jalview.binding.UserColourScheme\r
- vUserColourScheme)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColourSchemeList.insertElementAt(vUserColourScheme, index);\r
- } //-- void addUserColourScheme(int, jalview.binding.UserColourScheme)\r
-\r
- /**\r
- * Method enumerateUserColourScheme\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateUserColourScheme()\r
- {\r
- return _userColourSchemeList.elements();\r
- } //-- java.util.Enumeration enumerateUserColourScheme()\r
-\r
- /**\r
- * Method getUserColourScheme\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return UserColourScheme\r
- */\r
- public jalview.binding.UserColourScheme getUserColourScheme(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _userColourSchemeList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.binding.UserColourScheme) _userColourSchemeList.elementAt(\r
- index);\r
- } //-- jalview.binding.UserColourScheme getUserColourScheme(int)\r
-\r
- /**\r
- * Method getUserColourScheme\r
- *\r
- *\r
- *\r
- * @return UserColourScheme\r
- */\r
- public jalview.binding.UserColourScheme[] getUserColourScheme()\r
- {\r
- int size = _userColourSchemeList.size();\r
- jalview.binding.UserColourScheme[] mArray = new jalview.binding.\r
- UserColourScheme[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.binding.UserColourScheme) _userColourSchemeList.\r
- elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.UserColourScheme[] getUserColourScheme()\r
-\r
- /**\r
- * Method getUserColourSchemeCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getUserColourSchemeCount()\r
- {\r
- return _userColourSchemeList.size();\r
- } //-- int getUserColourSchemeCount()\r
-\r
- /**\r
- * Method removeAllUserColourScheme\r
- *\r
- */\r
- public void removeAllUserColourScheme()\r
- {\r
- _userColourSchemeList.removeAllElements();\r
- } //-- void removeAllUserColourScheme()\r
-\r
- /**\r
- * Method removeUserColourScheme\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return UserColourScheme\r
- */\r
- public jalview.binding.UserColourScheme removeUserColourScheme(int index)\r
- {\r
- java.lang.Object obj = _userColourSchemeList.elementAt(index);\r
- _userColourSchemeList.removeElementAt(index);\r
- return (jalview.binding.UserColourScheme) obj;\r
- } //-- jalview.binding.UserColourScheme removeUserColourScheme(int)\r
-\r
- /**\r
- * Method setUserColourScheme\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vUserColourScheme\r
- */\r
- public void setUserColourScheme(int index,\r
- jalview.binding.UserColourScheme\r
- vUserColourScheme)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _userColourSchemeList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _userColourSchemeList.setElementAt(vUserColourScheme, index);\r
- } //-- void setUserColourScheme(int, jalview.binding.UserColourScheme)\r
-\r
- /**\r
- * Method setUserColourScheme\r
- *\r
- *\r
- *\r
- * @param userColourSchemeArray\r
- */\r
- public void setUserColourScheme(jalview.binding.UserColourScheme[]\r
- userColourSchemeArray)\r
- {\r
- //-- copy array\r
- _userColourSchemeList.removeAllElements();\r
- for (int i = 0; i < userColourSchemeArray.length; i++)\r
- {\r
- _userColourSchemeList.addElement(userColourSchemeArray[i]);\r
- }\r
- } //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
-\r
-}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class Pdbentry.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Pdbentry implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _id\r
+ */\r
+ private java.lang.String _id;\r
+\r
+ /**\r
+ * Field _type\r
+ */\r
+ private java.lang.String _type;\r
+\r
+ /**\r
+ * Field _items\r
+ */\r
+ private java.util.Vector _items;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Pdbentry() {\r
+ super();\r
+ _items = new Vector();\r
+ } //-- jalview.binding.Pdbentry()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addPdbentryItem\r
+ * \r
+ * \r
+ * \r
+ * @param vPdbentryItem\r
+ */\r
+ public void addPdbentryItem(jalview.binding.PdbentryItem vPdbentryItem)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _items.addElement(vPdbentryItem);\r
+ } //-- void addPdbentryItem(jalview.binding.PdbentryItem) \r
+\r
+ /**\r
+ * Method addPdbentryItem\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbentryItem\r
+ */\r
+ public void addPdbentryItem(int index, jalview.binding.PdbentryItem vPdbentryItem)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _items.insertElementAt(vPdbentryItem, index);\r
+ } //-- void addPdbentryItem(int, jalview.binding.PdbentryItem) \r
+\r
+ /**\r
+ * Method enumeratePdbentryItem\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumeratePdbentryItem()\r
+ {\r
+ return _items.elements();\r
+ } //-- java.util.Enumeration enumeratePdbentryItem() \r
+\r
+ /**\r
+ * Returns the value of field 'id'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'id'.\r
+ */\r
+ public java.lang.String getId()\r
+ {\r
+ return this._id;\r
+ } //-- java.lang.String getId() \r
+\r
+ /**\r
+ * Method getPdbentryItem\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return PdbentryItem\r
+ */\r
+ public jalview.binding.PdbentryItem getPdbentryItem(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _items.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.PdbentryItem) _items.elementAt(index);\r
+ } //-- jalview.binding.PdbentryItem getPdbentryItem(int) \r
+\r
+ /**\r
+ * Method getPdbentryItem\r
+ * \r
+ * \r
+ * \r
+ * @return PdbentryItem\r
+ */\r
+ public jalview.binding.PdbentryItem[] getPdbentryItem()\r
+ {\r
+ int size = _items.size();\r
+ jalview.binding.PdbentryItem[] mArray = new jalview.binding.PdbentryItem[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.PdbentryItem) _items.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.PdbentryItem[] getPdbentryItem() \r
+\r
+ /**\r
+ * Method getPdbentryItemCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getPdbentryItemCount()\r
+ {\r
+ return _items.size();\r
+ } //-- int getPdbentryItemCount() \r
+\r
+ /**\r
+ * Returns the value of field 'type'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'type'.\r
+ */\r
+ public java.lang.String getType()\r
+ {\r
+ return this._type;\r
+ } //-- java.lang.String getType() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method removeAllPdbentryItem\r
+ * \r
+ */\r
+ public void removeAllPdbentryItem()\r
+ {\r
+ _items.removeAllElements();\r
+ } //-- void removeAllPdbentryItem() \r
+\r
+ /**\r
+ * Method removePdbentryItem\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return PdbentryItem\r
+ */\r
+ public jalview.binding.PdbentryItem removePdbentryItem(int index)\r
+ {\r
+ java.lang.Object obj = _items.elementAt(index);\r
+ _items.removeElementAt(index);\r
+ return (jalview.binding.PdbentryItem) obj;\r
+ } //-- jalview.binding.PdbentryItem removePdbentryItem(int) \r
+\r
+ /**\r
+ * Sets the value of field 'id'.\r
+ * \r
+ * @param id the value of field 'id'.\r
+ */\r
+ public void setId(java.lang.String id)\r
+ {\r
+ this._id = id;\r
+ } //-- void setId(java.lang.String) \r
+\r
+ /**\r
+ * Method setPdbentryItem\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vPdbentryItem\r
+ */\r
+ public void setPdbentryItem(int index, jalview.binding.PdbentryItem vPdbentryItem)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _items.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _items.setElementAt(vPdbentryItem, index);\r
+ } //-- void setPdbentryItem(int, jalview.binding.PdbentryItem) \r
+\r
+ /**\r
+ * Method setPdbentryItem\r
+ * \r
+ * \r
+ * \r
+ * @param pdbentryItemArray\r
+ */\r
+ public void setPdbentryItem(jalview.binding.PdbentryItem[] pdbentryItemArray)\r
+ {\r
+ //-- copy array\r
+ _items.removeAllElements();\r
+ for (int i = 0; i < pdbentryItemArray.length; i++) {\r
+ _items.addElement(pdbentryItemArray[i]);\r
+ }\r
+ } //-- void setPdbentryItem(jalview.binding.PdbentryItem) \r
+\r
+ /**\r
+ * Sets the value of field 'type'.\r
+ * \r
+ * @param type the value of field 'type'.\r
+ */\r
+ public void setType(java.lang.String type)\r
+ {\r
+ this._type = type;\r
+ } //-- void setType(java.lang.String) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.Serializable;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * Class PdbentryItem.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class PdbentryItem implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _propertyList\r
+ */\r
+ private java.util.Vector _propertyList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public PdbentryItem() {\r
+ super();\r
+ _propertyList = new Vector();\r
+ } //-- jalview.binding.PdbentryItem()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method addProperty\r
+ * \r
+ * \r
+ * \r
+ * @param vProperty\r
+ */\r
+ public void addProperty(jalview.binding.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _propertyList.addElement(vProperty);\r
+ } //-- void addProperty(jalview.binding.Property) \r
+\r
+ /**\r
+ * Method addProperty\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vProperty\r
+ */\r
+ public void addProperty(int index, jalview.binding.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _propertyList.insertElementAt(vProperty, index);\r
+ } //-- void addProperty(int, jalview.binding.Property) \r
+\r
+ /**\r
+ * Method enumerateProperty\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateProperty()\r
+ {\r
+ return _propertyList.elements();\r
+ } //-- java.util.Enumeration enumerateProperty() \r
+\r
+ /**\r
+ * Method getProperty\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Property\r
+ */\r
+ public jalview.binding.Property getProperty(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _propertyList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.binding.Property) _propertyList.elementAt(index);\r
+ } //-- jalview.binding.Property getProperty(int) \r
+\r
+ /**\r
+ * Method getProperty\r
+ * \r
+ * \r
+ * \r
+ * @return Property\r
+ */\r
+ public jalview.binding.Property[] getProperty()\r
+ {\r
+ int size = _propertyList.size();\r
+ jalview.binding.Property[] mArray = new jalview.binding.Property[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.binding.Property) _propertyList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.binding.Property[] getProperty() \r
+\r
+ /**\r
+ * Method getPropertyCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getPropertyCount()\r
+ {\r
+ return _propertyList.size();\r
+ } //-- int getPropertyCount() \r
+\r
+ /**\r
+ * Method removeAllProperty\r
+ * \r
+ */\r
+ public void removeAllProperty()\r
+ {\r
+ _propertyList.removeAllElements();\r
+ } //-- void removeAllProperty() \r
+\r
+ /**\r
+ * Method removeProperty\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return Property\r
+ */\r
+ public jalview.binding.Property removeProperty(int index)\r
+ {\r
+ java.lang.Object obj = _propertyList.elementAt(index);\r
+ _propertyList.removeElementAt(index);\r
+ return (jalview.binding.Property) obj;\r
+ } //-- jalview.binding.Property removeProperty(int) \r
+\r
+ /**\r
+ * Method setProperty\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vProperty\r
+ */\r
+ public void setProperty(int index, jalview.binding.Property vProperty)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _propertyList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _propertyList.setElementAt(vProperty, index);\r
+ } //-- void setProperty(int, jalview.binding.Property) \r
+\r
+ /**\r
+ * Method setProperty\r
+ * \r
+ * \r
+ * \r
+ * @param propertyArray\r
+ */\r
+ public void setProperty(jalview.binding.Property[] propertyArray)\r
+ {\r
+ //-- copy array\r
+ _propertyList.removeAllElements();\r
+ for (int i = 0; i < propertyArray.length; i++) {\r
+ _propertyList.addElement(propertyArray[i]);\r
+ }\r
+ } //-- void setProperty(jalview.binding.Property) \r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class Pdbids.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Pdbids extends Pdbentry \r
+implements java.io.Serializable\r
+{\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Pdbids() {\r
+ super();\r
+ } //-- jalview.binding.Pdbids()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Pdbids) Unmarshaller.unmarshal(jalview.binding.Pdbids.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class Property.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Property implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _name\r
+ */\r
+ private java.lang.String _name;\r
+\r
+ /**\r
+ * Field _value\r
+ */\r
+ private java.lang.String _value;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Property() {\r
+ super();\r
+ } //-- jalview.binding.Property()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'name'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'name'.\r
+ */\r
+ public java.lang.String getName()\r
+ {\r
+ return this._name;\r
+ } //-- java.lang.String getName() \r
+\r
+ /**\r
+ * Returns the value of field 'value'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'value'.\r
+ */\r
+ public java.lang.String getValue()\r
+ {\r
+ return this._value;\r
+ } //-- java.lang.String getValue() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Sets the value of field 'name'.\r
+ * \r
+ * @param name the value of field 'name'.\r
+ */\r
+ public void setName(java.lang.String name)\r
+ {\r
+ this._name = name;\r
+ } //-- void setName(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'value'.\r
+ * \r
+ * @param value the value of field 'value'.\r
+ */\r
+ public void setValue(java.lang.String value)\r
+ {\r
+ this._value = value;\r
+ } //-- void setValue(java.lang.String) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Property) Unmarshaller.unmarshal(jalview.binding.Property.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.binding;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class Setting.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Setting implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _type\r
+ */\r
+ private java.lang.String _type;\r
+\r
+ /**\r
+ * Field _colour\r
+ */\r
+ private int _colour;\r
+\r
+ /**\r
+ * keeps track of state for field: _colour\r
+ */\r
+ private boolean _has_colour;\r
+\r
+ /**\r
+ * Field _display\r
+ */\r
+ private boolean _display;\r
+\r
+ /**\r
+ * keeps track of state for field: _display\r
+ */\r
+ private boolean _has_display;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Setting() {\r
+ super();\r
+ } //-- jalview.binding.Setting()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method deleteColour\r
+ * \r
+ */\r
+ public void deleteColour()\r
+ {\r
+ this._has_colour= false;\r
+ } //-- void deleteColour() \r
+\r
+ /**\r
+ * Method deleteDisplay\r
+ * \r
+ */\r
+ public void deleteDisplay()\r
+ {\r
+ this._has_display= false;\r
+ } //-- void deleteDisplay() \r
+\r
+ /**\r
+ * Returns the value of field 'colour'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'colour'.\r
+ */\r
+ public int getColour()\r
+ {\r
+ return this._colour;\r
+ } //-- int getColour() \r
+\r
+ /**\r
+ * Returns the value of field 'display'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'display'.\r
+ */\r
+ public boolean getDisplay()\r
+ {\r
+ return this._display;\r
+ } //-- boolean getDisplay() \r
+\r
+ /**\r
+ * Returns the value of field 'type'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'type'.\r
+ */\r
+ public java.lang.String getType()\r
+ {\r
+ return this._type;\r
+ } //-- java.lang.String getType() \r
+\r
+ /**\r
+ * Method hasColour\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasColour()\r
+ {\r
+ return this._has_colour;\r
+ } //-- boolean hasColour() \r
+\r
+ /**\r
+ * Method hasDisplay\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasDisplay()\r
+ {\r
+ return this._has_display;\r
+ } //-- boolean hasDisplay() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Sets the value of field 'colour'.\r
+ * \r
+ * @param colour the value of field 'colour'.\r
+ */\r
+ public void setColour(int colour)\r
+ {\r
+ this._colour = colour;\r
+ this._has_colour = true;\r
+ } //-- void setColour(int) \r
+\r
+ /**\r
+ * Sets the value of field 'display'.\r
+ * \r
+ * @param display the value of field 'display'.\r
+ */\r
+ public void setDisplay(boolean display)\r
+ {\r
+ this._display = display;\r
+ this._has_display = true;\r
+ } //-- void setDisplay(boolean) \r
+\r
+ /**\r
+ * Sets the value of field 'type'.\r
+ * \r
+ * @param type the value of field 'type'.\r
+ */\r
+ public void setType(java.lang.String type)\r
+ {\r
+ this._type = type;\r
+ } //-- void setType(java.lang.String) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
*/\r
public class Alignment implements AlignmentI\r
{\r
+ protected Alignment dataset;\r
protected Vector sequences;\r
protected Vector groups = new Vector();\r
protected Vector superGroup = new Vector();\r
protected char gapCharacter = '-';\r
- protected boolean isNucleotide = true;\r
-\r
+ protected int type = NUCLEOTIDE;\r
+ public static final int PROTEIN = 0;\r
+ public static final int NUCLEOTIDE = 1;\r
\r
/** DOCUMENT ME!! */\r
public AlignmentAnnotation[] annotations;\r
\r
- /** DOCUMENT ME!! */\r
- public boolean featuresAdded = false;\r
-\r
/** Make an alignment from an array of Sequences.\r
*\r
* @param sequences\r
*/\r
public Alignment(SequenceI[] seqs)\r
{\r
- int i=0, iSize = seqs.length, j, jSize;\r
- while(isNucleotide && i<iSize)\r
- {\r
- jSize = seqs[i].getLength();\r
- for(j=0; j<jSize; j++)\r
- {\r
- if(!jalview.schemes.ResidueProperties.nucleotideHash.containsKey(seqs[i].getSequence(j, j+1))\r
- && !jalview.util.Comparison.isGap(seqs[i].getSequence().charAt(j)))\r
- {\r
- isNucleotide = false;\r
- break;\r
- }\r
- }\r
- i++;\r
- }\r
+ int i=0;\r
+\r
+ if( jalview.util.Comparison.isNucleotide(seqs))\r
+ type = NUCLEOTIDE;\r
+ else\r
+ type = PROTEIN;\r
\r
sequences = new Vector();\r
\r
\r
while (i < sequences.size())\r
{\r
- SequenceI s = getSequenceAt(i);\r
-\r
- if (s.getName().equals(name))\r
+ if (getSequenceAt(i).getName().equals(name))\r
{\r
- return s;\r
+ return getSequenceAt(i);\r
}\r
\r
i++;\r
return null;\r
}\r
\r
- /** */\r
- public SequenceI findbyDisplayId(String name)\r
- {\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- SequenceI s = getSequenceAt(i);\r
-\r
- if (s.getDisplayId().equals(name))\r
- {\r
- return s;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return null;\r
- }\r
\r
/** */\r
public int findIndex(SequenceI s)\r
aSize = annotations.length + 1;\r
}\r
\r
+\r
AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
int i = 0;\r
\r
\r
public void setNucleotide(boolean b)\r
{\r
- isNucleotide = b;\r
+ if(b)\r
+ type = NUCLEOTIDE;\r
+ else\r
+ type = PROTEIN;\r
}\r
\r
public boolean isNucleotide()\r
{\r
- return isNucleotide;\r
+ if(type==NUCLEOTIDE)\r
+ return true;\r
+ else\r
+ return false;\r
}\r
+\r
+ public void setDataset(Alignment data)\r
+ {\r
+ if(dataset==null && data==null)\r
+ {\r
+ // Create a new dataset for this alignment.\r
+ // Can only be done once, if dataset is not null\r
+ // This will not be performed\r
+ Sequence[] seqs = new Sequence[getHeight()];\r
+ for (int i = 0; i < getHeight(); i++)\r
+ {\r
+\r
+ seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
+ AlignSeq.extractGaps(\r
+ jalview.util.Comparison.GapChars,\r
+ getSequenceAt(i).getSequence()\r
+ ),\r
+ getSequenceAt(i).getStart(),\r
+ getSequenceAt(i).getEnd());\r
+\r
+ getSequenceAt(i).setDatasetSequence(seqs[i]);\r
+ }\r
+\r
+ dataset = new Alignment(seqs);\r
+ }\r
+ else if(dataset==null && data!=null)\r
+ {\r
+ dataset = data;\r
+ }\r
+ }\r
+\r
+ public Alignment getDataset()\r
+ {\r
+ return dataset;\r
+ }\r
+\r
}\r
*/\r
public SequenceI findName(String name);\r
\r
- /**\r
- * Finds sequence in alignment using full displayId as query.\r
- *\r
- * @param name displayId, ie <em>NAME/25-100</em>\r
- *\r
- * @return Sequence matching query, if found. If not found returns null.\r
- */\r
- public SequenceI findbyDisplayId(String name);\r
\r
/**\r
* Finds index of a given sequence in the alignment.\r
*/\r
public void setNucleotide(boolean b);\r
\r
+\r
+ public Alignment getDataset();\r
+\r
+ public void setDataset(Alignment dataset);\r
+\r
+\r
}\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+public class DBRefEntry\r
+{\r
+ String source, version, accessionId;\r
+\r
+ public DBRefEntry(String source, String version, String accessionId)\r
+ {\r
+ this.source = source;\r
+ this.version = version;\r
+ this.accessionId = accessionId;\r
+ }\r
+\r
+ public String getSource()\r
+ { return source; }\r
+\r
+ public String getVersion()\r
+ { return version; }\r
+\r
+ public String getAccessionId()\r
+ { return accessionId; }\r
+\r
+}\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+import java.util.*;\r
+public class PDBEntry\r
+{\r
+ String type;\r
+ String id;\r
+ Hashtable properties;\r
+\r
+ public PDBEntry()\r
+ { }\r
+\r
+ public void setType(String type)\r
+ { this.type = type; }\r
+\r
+ public String getType()\r
+ { return type; }\r
+\r
+ public void setId(String id)\r
+ { this.id = id; }\r
+\r
+ public String getId()\r
+ { return id; }\r
+\r
+ public void setProperty(Hashtable property)\r
+ {\r
+ this.properties = property;\r
+ }\r
+\r
+ public Hashtable getProperty()\r
+ {\r
+ return properties;\r
+ }\r
+\r
+\r
+}\r
--- /dev/null
+package jalview.datamodel;\r
+import java.util.*;\r
+\r
+public class Provenance\r
+{\r
+ Vector entries = new Vector();\r
+ public Provenance()\r
+ {\r
+\r
+ }\r
+\r
+ public ProvenanceEntry[] getEntries()\r
+ {\r
+ ProvenanceEntry [] ret = new ProvenanceEntry[entries.size()];\r
+ for(int i=0; i<entries.size(); i++)\r
+ ret[i] = (ProvenanceEntry)entries.elementAt(i);\r
+ return ret;\r
+ }\r
+\r
+ public void addEntry(String user, String action, java.util.Date date, String id)\r
+ {\r
+ entries.addElement( new ProvenanceEntry(user,action,date,id));\r
+ }\r
+\r
+}\r
+\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+public class ProvenanceEntry\r
+{\r
+ String user, action, id;\r
+ java.util.Date date;\r
+ public ProvenanceEntry(String u, String a, java.util.Date d, String i)\r
+ {\r
+ user = u; action = a; date = d; id = i;\r
+ }\r
+\r
+ public String getUser()\r
+ {return user;}\r
+\r
+ public String getAction()\r
+ {return action;}\r
+\r
+ public java.util.Date getDate()\r
+ {return date;}\r
+\r
+ public String getID()\r
+ {return id;}\r
+}\r
*/\r
public class Sequence implements SequenceI\r
{\r
- protected String name;\r
- protected String sequence;\r
- protected String description;\r
- protected int start;\r
- protected int end;\r
- protected String displayId;\r
- protected Color color = Color.white;\r
- String pdbId;\r
+ SequenceI datasetSequence;\r
+ String name;\r
+ String sequence;\r
+ String description;\r
+ int start;\r
+ int end;\r
+ Color color = Color.white;\r
+ Vector pdbIds;\r
+ String vamsasId;\r
+ Vector dbrefs;\r
+\r
\r
/** DOCUMENT ME!! */\r
- public Vector sequenceFeatures = new Vector();\r
+ public Vector sequenceFeatures;\r
\r
/**\r
* Creates a new Sequence object.\r
this.start = start;\r
this.end = end;\r
\r
+ parseId();\r
+\r
+ checkValidRange();\r
+ }\r
+\r
+ static com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(\r
+ "[/][0-9]{1,}[-][0-9]{1,}$");\r
+ static com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(\r
+ "[0-9]{1,}$");\r
+\r
+ void parseId()\r
+ {\r
+ // Does sequence have the /start-end signiature?\r
+ if(limitrx.search(name))\r
+ {\r
+ name = limitrx.left();\r
+ endrx.search(limitrx.stringMatched());\r
+ setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 )));\r
+ setEnd( Integer.parseInt( endrx.stringMatched() ));\r
+ }\r
+ }\r
+\r
+ void checkValidRange()\r
+ {\r
if (end < 1)\r
{\r
int endRes = 0;\r
this.end = endRes;\r
}\r
\r
- setDisplayId();\r
}\r
\r
/**\r
*/\r
public Sequence(String name, String sequence)\r
{\r
- this(name, sequence, 1, sequence.length());\r
+ this(name, sequence, 1, -1);\r
}\r
\r
/**\r
sequenceFeatures = v;\r
}\r
\r
+ public void addSequenceFeature(SequenceFeature sf)\r
+ {\r
+ if(sequenceFeatures==null)\r
+ sequenceFeatures = new Vector();\r
+\r
+ sequenceFeatures.addElement(sf);\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
return sequenceFeatures;\r
}\r
\r
+ public void addPDBId(PDBEntry entry)\r
+ {\r
+ if(pdbIds == null)\r
+ pdbIds = new Vector();\r
+\r
+ pdbIds.addElement(entry);\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @param id DOCUMENT ME!\r
*/\r
- public void setPDBId(String id)\r
+ public void setPDBId(Vector id)\r
{\r
- pdbId = id;\r
+ pdbIds = id;\r
}\r
\r
/**\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public String getPDBId()\r
+ public Vector getPDBId()\r
{\r
- return pdbId;\r
+ return pdbIds;\r
}\r
\r
/**\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public String getDisplayId()\r
+ public String getDisplayId(boolean jvsuffix)\r
{\r
- return displayId;\r
- }\r
+ StringBuffer result = new StringBuffer(name);\r
+ if (jvsuffix)\r
+ {\r
+ result.append("/" + start + "-" + end);\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void setDisplayId()\r
- {\r
- displayId = name + "/" + start + "-" + end;\r
+ return result.toString();\r
}\r
\r
/**\r
*/\r
public void setName(String name)\r
{\r
- this.name = name;\r
- setDisplayId();\r
+ this.name = name;\r
+ this.parseId();\r
}\r
\r
/**\r
*/\r
public String getName()\r
{\r
- return this.name;\r
+ return this.name;\r
}\r
\r
/**\r
public void setStart(int start)\r
{\r
this.start = start;\r
- setDisplayId();\r
}\r
\r
/**\r
public void setEnd(int end)\r
{\r
this.end = end;\r
- setDisplayId();\r
}\r
\r
/**\r
public void setSequence(String seq)\r
{\r
this.sequence = seq;\r
+ checkValidRange();\r
}\r
\r
/**\r
\r
while ((i < sequence.length()) && (j <= end) && (j <= pos))\r
{\r
- char c = sequence.charAt(i);\r
-\r
- if (!jalview.util.Comparison.isGap((c)))\r
+ if (!jalview.util.Comparison.isGap(sequence.charAt(i)))\r
{\r
j++;\r
}\r
\r
while ((j < i) && (j < sequence.length()))\r
{\r
- char c = sequence.charAt(j);\r
-\r
- if (!jalview.util.Comparison.isGap((c)))\r
+ if (!jalview.util.Comparison.isGap((sequence.charAt(j))))\r
{\r
pos++;\r
}\r
{\r
return color;\r
}\r
+\r
+ public String getVamsasId()\r
+ {\r
+ return vamsasId;\r
+ }\r
+\r
+ public void setVamsasId(String id)\r
+ {\r
+ vamsasId = id;\r
+ }\r
+\r
+ public void setDBRef(Vector dbref)\r
+ {\r
+ dbrefs = dbref;\r
+ }\r
+ public Vector getDBRef()\r
+ {\r
+ return dbrefs;\r
+ }\r
+\r
+ public void addDBRef(DBRefEntry entry)\r
+ {\r
+ if(dbrefs == null)\r
+ dbrefs = new Vector();\r
+\r
+ dbrefs.addElement(entry);\r
+ }\r
+\r
+ public void setDatasetSequence(SequenceI seq)\r
+ {\r
+ datasetSequence = seq;\r
+ }\r
+\r
+ public SequenceI getDatasetSequence()\r
+ {\r
+ return datasetSequence;\r
+ }\r
+\r
}\r
*/\r
public class SequenceFeature\r
{\r
+ int position;\r
int begin;\r
int end;\r
String type;\r
String description;\r
String status;\r
\r
- /**\r
- * Creates a new SequenceFeature object.\r
- */\r
public SequenceFeature()\r
+ {}\r
+\r
+ public SequenceFeature(String type, String desc, String status, int begin, int end)\r
{\r
+ this.type = type;\r
+ this.description = desc;\r
+ this.status = status;\r
+ this.position = begin;\r
+ this.begin = begin;\r
+ this.end = end;\r
}\r
\r
- /**\r
- * Creates a new SequenceFeature object.\r
- *\r
- * @param type DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- * @param description DOCUMENT ME!\r
- * @param status DOCUMENT ME!\r
- */\r
- public SequenceFeature(String type, int start, int end, String description,\r
- String status)\r
+ public int getPosition()\r
{\r
- this.type = type;\r
- this.begin = start;\r
- this.end = end;\r
- this.description = description;\r
- this.status = status;\r
+ return position;\r
}\r
\r
+ public void setPosition(int pos)\r
+ {\r
+ position = pos;\r
+ begin = pos;\r
+ end = pos;\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public int getStart()\r
+ public int getBegin()\r
{\r
return begin;\r
}\r
\r
+ public void setBegin(int start)\r
+ {\r
+ this.begin = start;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
return end;\r
}\r
\r
+ public void setEnd(int end)\r
+ {\r
+ this.end = end;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
return type;\r
}\r
\r
+ public void setType(String type)\r
+ {\r
+ this.type = type;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
return description;\r
}\r
\r
+ public void setDescription(String desc)\r
+ {\r
+ description = desc;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
return status;\r
}\r
\r
- /*\r
- <xs:enumeration value="active site" />\r
- <xs:enumeration value="binding site" />\r
- <xs:enumeration value="calcium-binding region" />\r
- <xs:enumeration value="chain" />\r
- <xs:enumeration value="cross-link" />\r
- <xs:enumeration value="disulfide bond" />\r
- <xs:enumeration value="DNA-binding region" />\r
- <xs:enumeration value="domain" />\r
- <xs:enumeration value="glycosylation site" />\r
- <xs:enumeration value="helix" />\r
- <xs:enumeration value="initiator methionine" />\r
- <xs:enumeration value="lipid moiety-binding region" />\r
- <xs:enumeration value="metal ion-binding site" />\r
- <xs:enumeration value="modified residue" />\r
- <xs:enumeration value="mutagenesis site" />\r
- <xs:enumeration value="non-consecutive residues" />\r
- <xs:enumeration value="non-terminal residue" />\r
- <xs:enumeration value="nucleotide phosphate-binding region" />\r
- <xs:enumeration value="peptide" />\r
- <xs:enumeration value="propeptide" />\r
- <xs:enumeration value="repeat" />\r
- <xs:enumeration value="selenocysteine" />\r
- <xs:enumeration value="sequence conflict" />\r
- <xs:enumeration value="sequence variant" />\r
- <xs:enumeration value="signal peptide" />\r
- <xs:enumeration value="similar" />\r
- <xs:enumeration value="site" />\r
- <xs:enumeration value="splice variant" />\r
- <xs:enumeration value="strand" />\r
- <xs:enumeration value="thioether bond" />\r
- <xs:enumeration value="thiolester bond" />\r
- <xs:enumeration value="transit peptide" />\r
- <xs:enumeration value="transmembrane region" />\r
- <xs:enumeration value="turn" />\r
- <xs:enumeration value="unsure residue" />\r
- <xs:enumeration value="zinc finger region" />\r
- */\r
+ public void setStatus(String status)\r
+ {\r
+ this.status = status;\r
+ }\r
+\r
}\r
*/\r
public String getName();\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public String getDisplayId();\r
+ public String getDisplayId(boolean jvsuffix);\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @param id DOCUMENT ME!\r
*/\r
- public void setPDBId(String id);\r
+ public void setPDBId(Vector ids);\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public String getPDBId();\r
+ public Vector getPDBId();\r
+\r
+ public void addPDBId(PDBEntry entry);\r
+\r
+ public String getVamsasId();\r
+\r
+ public void setVamsasId(String id);\r
+\r
+ public void setDBRef(Vector dbs);\r
+\r
+ public Vector getDBRef();\r
+\r
+ public void addDBRef(DBRefEntry entry);\r
+\r
+ public void addSequenceFeature(SequenceFeature sf);\r
+\r
+ public void setDatasetSequence(SequenceI seq);\r
+\r
+ public SequenceI getDatasetSequence();\r
}\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+import java.util.*;\r
+\r
+public class UniprotEntry\r
+{\r
+\r
+ UniprotSequence sequence;\r
+ Vector name;\r
+ Vector accession;\r
+ Vector feature;\r
+ Vector dbrefs;\r
+ Vector proteinName;\r
+\r
+ public void setAccession(Vector items)\r
+ {\r
+ accession = items;\r
+ }\r
+\r
+ public void setFeature(Vector items)\r
+ {\r
+ feature = items;\r
+ }\r
+\r
+ public Vector getFeature() {\r
+ return feature;\r
+ }\r
+\r
+\r
+ public Vector getAccession()\r
+ {\r
+ return accession;\r
+ }\r
+\r
+ public void setProteinName(Vector items)\r
+ {\r
+ proteinName = items;\r
+ }\r
+\r
+ public Vector getProteinName()\r
+ {\r
+ return proteinName;\r
+ }\r
+\r
+ public void setName(Vector na)\r
+ {\r
+ name = na;\r
+ }\r
+ public Vector getName()\r
+ {\r
+ return name;\r
+ }\r
+\r
+ public UniprotSequence getUniprotSequence()\r
+ {\r
+ return sequence;\r
+ }\r
+\r
+ public void setUniprotSequence(UniprotSequence seq)\r
+ {\r
+ sequence = seq;\r
+ }\r
+\r
+ public Vector getDbReference()\r
+ {\r
+ return dbrefs;\r
+ }\r
+\r
+ public void setDbReference(Vector dbref)\r
+ {\r
+ this.dbrefs = dbref;\r
+ }\r
+\r
+}\r
--- /dev/null
+package jalview.datamodel;\r
+import java.util.Vector;\r
+\r
+public class UniprotFile\r
+{\r
+ Vector _items;\r
+\r
+ public void setUniprotEntries(Vector items) {\r
+ _items = items;\r
+ }\r
+\r
+ public Vector getUniprotEntries() {\r
+ return _items;\r
+ }\r
+}\r
--- /dev/null
+package jalview.datamodel;\r
+\r
+public class UniprotSequence\r
+{\r
+ /**\r
+ * internal content storage\r
+ */\r
+ private java.lang.String _content = "";\r
+\r
+ public void setContent(String seq)\r
+ {\r
+ StringBuffer sb = new StringBuffer();\r
+ for(int i=0; i<seq.length(); i++)\r
+ if(seq.charAt(i)!=' ')\r
+ {\r
+ sb.append(seq.charAt(i));\r
+ }\r
+ _content = sb.toString();\r
+ }\r
+\r
+ public String getContent()\r
+ { return _content; }\r
+\r
+}\r
Vector headers;\r
long start;\r
long end;\r
+ boolean jvSuffix = true;\r
\r
/**\r
* Creates a new AlignFile object.\r
* Print out in alignment file format the Sequences in the seqs Vector.\r
*/\r
public abstract String print();\r
+\r
+ public void addJVSuffix(boolean b)\r
+ {\r
+ jvSuffix = b;\r
+ }\r
+\r
+ /**\r
+ * A general parser for ids.\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
+ Sequence parseId(String id)\r
+ {\r
+ Sequence seq = null;\r
+ id = id.trim();\r
+ int space = id.indexOf(" ");\r
+ if(space>-1)\r
+ {\r
+ seq = new Sequence(id.substring(0, space),"");\r
+ seq.setDescription(id.substring(space+1));\r
+ }\r
+ else\r
+ {\r
+ seq = new Sequence(id, "");\r
+ }\r
+\r
+ return seq;\r
+ }\r
+\r
+ /**\r
+ * Creates the output id.\r
+ * Adds prefix Uniprot format source|id\r
+ * And suffix Jalview /start-end\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
+ String printId(SequenceI seq)\r
+ {\r
+ return seq.getDisplayId(jvSuffix);\r
+ }\r
+\r
}\r
--- /dev/null
+ /*\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
+ package jalview.io;\r
+\r
+ import jalview.datamodel.*;\r
+\r
+ import java.util.Vector;\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+ public class AppletFormatAdapter\r
+ {\r
+ /** DOCUMENT ME!! */\r
+ public static final Vector formats = new Vector();\r
+\r
+ static\r
+ {\r
+ formats.addElement("BLC");\r
+ formats.addElement("CLUSTAL");\r
+ formats.addElement("FASTA");\r
+ formats.addElement("MSF");\r
+ formats.addElement("PileUp");\r
+ formats.addElement("PIR");\r
+ formats.addElement("PFAM");\r
+ }\r
+\r
+ AlignFile afile = null;\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ * @param format DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceI[] readFile(String inFile, String type, String format)\r
+ {\r
+ try\r
+ {\r
+ if (format.equals("FASTA"))\r
+ {\r
+ afile = new FastaFile(inFile, type);\r
+ }\r
+ else if (format.equals("MSF"))\r
+ {\r
+ afile = new MSFfile(inFile, type);\r
+ }\r
+ else if (format.equals("PileUp"))\r
+ {\r
+ afile = new PileUpfile(inFile, type);\r
+ }\r
+ else if (format.equals("CLUSTAL"))\r
+ {\r
+ afile = new ClustalFile(inFile, type);\r
+ }\r
+ else if (format.equals("BLC"))\r
+ {\r
+ afile = new BLCFile(inFile, type);\r
+ }\r
+ else if (format.equals("PIR"))\r
+ {\r
+ afile = new PIRFile(inFile, type);\r
+ }\r
+ else if (format.equals("PFAM"))\r
+ {\r
+ afile = new PfamFile(inFile, type);\r
+ }\r
+\r
+ return afile.getSeqsAsArray();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ System.err.println("Failed to read alignment using the '" + format +\r
+ "' reader.\n"+e);\r
+\r
+ // Finally test if the user has pasted just the sequence, no id\r
+ if(type.equalsIgnoreCase("Paste"))\r
+ {\r
+ try{\r
+ // Possible sequence is just residues with no label\r
+ afile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");\r
+ return afile.getSeqsAsArray();\r
+ }catch(Exception ex)\r
+ {\r
+ System.err.println("Failed to read alignment using the 'FASTA' reader.\n"+e);\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ }\r
+ }\r
+\r
+ return null;\r
+ }\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param format DOCUMENT ME!\r
+ * @param seqs DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String formatSequences(String format,\r
+ Vector seqs,\r
+ boolean jvsuffix)\r
+ {\r
+ SequenceI[] s = new SequenceI[seqs.size()];\r
+\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ s[i] = (SequenceI) seqs.elementAt(i);\r
+\r
+ try\r
+ {\r
+ AlignFile afile = null;\r
+\r
+ if (format.equalsIgnoreCase("FASTA"))\r
+ {\r
+ afile = new FastaFile();\r
+ }\r
+ else if (format.equalsIgnoreCase("MSF"))\r
+ {\r
+ afile = new MSFfile();\r
+ }\r
+ else if (format.equalsIgnoreCase("PileUp"))\r
+ {\r
+ afile = new PileUpfile();\r
+ }\r
+ else if (format.equalsIgnoreCase("CLUSTAL"))\r
+ {\r
+ afile = new ClustalFile();\r
+ }\r
+ else if (format.equalsIgnoreCase("BLC"))\r
+ {\r
+ afile = new BLCFile();\r
+ }\r
+ else if (format.equalsIgnoreCase("PIR"))\r
+ {\r
+ afile = new PIRFile();\r
+ }\r
+ else if (format.equalsIgnoreCase("PFAM"))\r
+ {\r
+ afile = new PfamFile();\r
+ }\r
+\r
+ afile.addJVSuffix(jvsuffix);\r
+\r
+ afile.setSeqs(s);\r
+\r
+ return afile.print();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ System.err.println("Failed to write alignment as a '" + format +\r
+ "' file\n");\r
+ e.printStackTrace();\r
+ }\r
+\r
+ return null;\r
+ }\r
+ }\r
\r
if (abracket > -1)\r
{\r
- if (line.indexOf(" ") > -1) //\r
- {\r
- ///Colur it be this format?\r
- //>54402046 0 1 137 137:\r
- // or this??\r
- // 1 >L1H14 30539 343\r
- try\r
- {\r
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf(" ", abracket + 1)));\r
-\r
- // remove p Value\r
- line = line.substring(abracket + 1);\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
-\r
- int value = Integer.parseInt(line.substring(0,\r
- line.indexOf(" ")));\r
- starts.addElement(value + "");\r
- line = line.substring(line.indexOf(" ") + 1);\r
- line = line.trim();\r
- value = Integer.parseInt(line.substring(0,\r
- line.indexOf(" ")));\r
- ends.addElement(value + "");\r
- }\r
- catch (Exception ex)\r
- {\r
- System.err.println("Error during blockfile read.");\r
- ex.printStackTrace();\r
- starts.addElement("1");\r
- ends.addElement("-1");\r
- }\r
- }\r
- else\r
- {\r
- if (line.indexOf("/") > -1)\r
- {\r
- ids.addElement(line.substring(abracket + 1,\r
- line.indexOf("/")));\r
- line = line.substring(line.indexOf("/") + 1);\r
- starts.addElement(line.substring(0,\r
- line.indexOf("-")));\r
- ends.addElement(line.substring(line.indexOf("-") +\r
- 1));\r
- }\r
- else\r
- {\r
- ids.addElement(line.substring(abracket + 1));\r
- starts.addElement("1");\r
- ends.addElement("-1");\r
- }\r
- }\r
+ if (line.indexOf(" ") > -1) //\r
+ {\r
+ line = line.substring(abracket + 1,\r
+ line.indexOf(" ", abracket + 1));\r
+ }\r
+ else\r
+ line = line.substring(abracket+1);\r
+\r
+\r
+ Sequence seq = parseId(line);\r
+ ids.addElement(seq.getName());\r
+ starts.addElement(seq.getStart() + "");\r
+ ends.addElement(seq.getEnd() + "");\r
}\r
}\r
while (!idsFound);\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static String print(SequenceI[] s)\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer();\r
-\r
+ /**\r
+ * A general parser for ids. Will look for dbrefs in\r
+ * Uniprot format source|id\r
+ * And also Jalview /start-end\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
int i = 0;\r
int max = -1;\r
\r
while ((i < s.length) && (s[i] != null))\r
{\r
- out.append(">" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd() + "\n");\r
+ out.append(">" + printId(s[i]) +"\n");\r
\r
if (s[i].getSequence().length() > max)\r
{\r
public class ClustalFile\r
extends AlignFile\r
{\r
- Vector ids;\r
\r
public ClustalFile()\r
{\r
public void initData()\r
{\r
super.initData();\r
- ids = new Vector();\r
}\r
\r
public void parse()\r
\r
Vector headers = new Vector();\r
Hashtable seqhash = new Hashtable();\r
-\r
- String line;\r
+ StringBuffer tempseq;\r
+ String line, id;\r
+ StringTokenizer str;\r
\r
try\r
{\r
{\r
if (line.indexOf(" ") != 0)\r
{\r
- StringTokenizer str = new StringTokenizer(line, " ");\r
- String id = "";\r
+ str = new StringTokenizer(line, " ");\r
\r
if (str.hasMoreTokens())\r
{\r
id = str.nextToken();\r
\r
- if (id.equals("CLUSTAL"))\r
+ if (id.equalsIgnoreCase("CLUSTAL"))\r
{\r
flag = true;\r
}\r
{\r
if (flag)\r
{\r
- StringBuffer tempseq;\r
-\r
if (seqhash.containsKey(id))\r
{\r
tempseq = (StringBuffer) seqhash.get(id);\r
}\r
}\r
}\r
+ else\r
+ flag = true;\r
}\r
}\r
}\r
//Add sequences to the hash\r
for (i = 0; i < headers.size(); i++)\r
{\r
- int start = 1;\r
- int end = -1;\r
-\r
if (seqhash.get(headers.elementAt(i)) != null)\r
{\r
if (maxLength < seqhash.get(headers.elementAt(i)).toString()\r
.length();\r
}\r
\r
- String head = headers.elementAt(i).toString();\r
-\r
- if (head.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- ids.addElement(st.nextToken());\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken())\r
- .intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- else\r
- {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
- }\r
- else\r
- {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
-\r
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqhash.get(headers.elementAt(i).\r
- toString())\r
- .toString(), start, end);\r
+ Sequence newSeq = parseId(headers.elementAt(i).toString());\r
+ newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString() );\r
\r
seqs.addElement(newSeq);\r
}\r
return print(getSeqsAsArray());\r
}\r
\r
- public static String print(SequenceI[] s)\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer("CLUSTAL\n\n");\r
\r
\r
while ( (i < s.length) && (s[i] != null))\r
{\r
- String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd();\r
+ String tmp = printId(s[i]);\r
\r
if (s[i].getSequence().length() > max)\r
{\r
\r
while ( (j < s.length) && (s[j] != null))\r
{\r
- out.append(new Format("%-" + maxid + "s").form(s[j].getName() +\r
- "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+ out.append(new Format("%-" + maxid + "s").form( printId(s[j]) + " "));\r
\r
int start = i * len;\r
int end = start + len;\r
*/\r
package jalview.io;\r
\r
+import java.io.*;\r
+\r
import org.apache.axis.AxisFault;\r
import org.apache.axis.client.*;\r
import org.apache.axis.encoding.XMLType;\r
}\r
}\r
\r
+ public static void main (String [] args)\r
+ {\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String[] result = ebi.fetchData("uniprot:25K89D_SARPE;G6PblobD_HUMAN",\r
+ "xml", null);\r
+\r
+ try{\r
+ java.io.PrintWriter out = new java.io.PrintWriter(\r
+ new java.io.FileWriter("out.xml"));\r
+\r
+\r
+ for(int i=0; i<result.length; i++)\r
+ {\r
+ out.println(result[i]);\r
+ }\r
+ out.close();\r
+ }catch(Exception ex){ex.printStackTrace();}\r
+\r
+ }\r
+\r
+\r
+ public File fetchDataAsFile(String ids, String f, String s)\r
+ {\r
+ String [] data = fetchData(ids, f, s);\r
+ File outFile = null;\r
+ try{\r
+ outFile = File.createTempFile("jalview", ".xml");\r
+ outFile.deleteOnExit();\r
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
+ int index=0;\r
+ while( index < data.length )\r
+ {\r
+ out.println(data[index]);\r
+ index++;\r
+ }\r
+ out.close();\r
+ }catch(Exception ex){}\r
+ return outFile;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
package jalview.io;\r
\r
-import jalview.analysis.*;\r
-\r
import jalview.datamodel.*;\r
\r
import java.io.*;\r
\r
-import java.util.*;\r
-\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public void parse() throws IOException\r
{\r
- String id = "";\r
- StringBuffer seq = new StringBuffer();\r
+ StringBuffer sb = new StringBuffer();\r
int count = 0;\r
\r
- int sstart = 0;\r
- int send = 0;\r
-\r
String line;\r
+ Sequence seq = null;\r
\r
while ((line = nextLine()) != null)\r
{\r
if (line.length() > 0)\r
{\r
- // Do we have an id line?\r
- // JBPNote - this code needs to be standardised to EBI/whatever for the\r
- // >dbref/dbref/dbref|refid1|refid2|refid3 'human-readable' style of naming (should it really exist)\r
- if (line.substring(0, 1).equals(">"))\r
+ if (line.charAt(0)=='>')\r
{\r
if (count != 0)\r
{\r
- if (sstart != 0)\r
- {\r
- seqs.addElement(new Sequence(id, seq.toString(),\r
- sstart, send));\r
- }\r
- else\r
- {\r
- seqs.addElement(new Sequence(id, seq.toString(), 1,\r
- seq.length()));\r
- }\r
+ seq.setSequence(sb.toString());\r
+ seqs.addElement(seq);\r
}\r
\r
- count++;\r
-\r
- StringTokenizer str = new StringTokenizer(line, " ");\r
-\r
- id = str.nextToken();\r
- id = id.substring(1);\r
-\r
- com.stevesoft.pat.Regex dbId = new com.stevesoft.pat.Regex(\r
- "[A-Za-z-]+/?[A-Za-z-]+\\|(\\w+)\\|(.+)");\r
-\r
- // JBPNote At the moment - we don't get rid of the friendly names but this\r
- // behaviour is probably wrong in the long run.\r
- if (dbId.search(id))\r
- {\r
- String dbid = dbId.stringMatched(1);\r
- String idname = dbId.stringMatched(2);\r
-\r
- if ((idname.length() > 0) &&\r
- (idname.indexOf("_") > -1))\r
- {\r
- id = idname; // use the friendly name - apparently no dbid\r
- }\r
- else if (dbid.length() > 1)\r
- {\r
- id = dbid; // ignore the friendly name - we lose uniprot accession ID otherwise\r
- }\r
- }\r
-\r
- if (id.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(id, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- id = st.nextToken();\r
-\r
- String tmp = st.nextToken();\r
+ seq = parseId(line.substring(1));\r
\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- sstart = Integer.valueOf(st.nextToken())\r
- .intValue();\r
- send = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- }\r
-\r
- seq = new StringBuffer();\r
+ count++;\r
+ sb = new StringBuffer();\r
}\r
else\r
{\r
- seq = seq.append(line);\r
+ sb.append(line);\r
}\r
}\r
}\r
\r
if (count > 0)\r
{\r
- if (!isValidProteinSequence(seq.toString().toUpperCase()))\r
+ if (!isValidProteinSequence(sb.toString().toUpperCase()))\r
{\r
throw new IOException("Invalid protein sequence");\r
}\r
\r
- if (sstart != 0)\r
- {\r
- seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),\r
- sstart, send));\r
- }\r
- else\r
- {\r
- seqs.addElement(new Sequence(id, seq.toString().toUpperCase(),\r
- 1, seq.length()));\r
- }\r
+ seq.setSequence(sb.toString());\r
+ seqs.addElement(seq);\r
}\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String print(SequenceI[] s)\r
- {\r
- return print(s, 72);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param len DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String print(SequenceI[] s, int len)\r
- {\r
- return print(s, len, true);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- * @param len DOCUMENT ME!\r
- * @param gaps DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String print(SequenceI[] s, int len, boolean gaps)\r
- {\r
- return print(s, len, gaps, true);\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static String print(SequenceI[] s, int len, boolean gaps,\r
- boolean displayId)\r
+ public String print(SequenceI[] s)\r
{\r
+ int len = 72;\r
StringBuffer out = new StringBuffer();\r
int i = 0;\r
\r
while ((i < s.length) && (s[i] != null))\r
{\r
- String seq = "";\r
-\r
- if (gaps)\r
- {\r
- seq = s[i].getSequence();\r
- }\r
- else\r
- {\r
- seq = AlignSeq.extractGaps("-. ", s[i].getSequence());\r
- }\r
+ out.append(">" + printId(s[i]));\r
+ if(s[i].getDescription()!=null)\r
+ out.append(" "+s[i].getDescription());\r
\r
- // used to always put this here: + "/" + s[i].getStart() + "-" + s[i].getEnd() +\r
- out.append(">" +\r
- ((displayId) ? s[i].getDisplayId() : s[i].getName()) + "\n");\r
+ out.append("\n");\r
\r
- int nochunks = (seq.length() / len) + 1;\r
+ int nochunks = (s[i].getLength() / len) + 1;\r
\r
for (int j = 0; j < nochunks; j++)\r
{\r
int start = j * len;\r
int end = start + len;\r
\r
- if (end < seq.length())\r
+ if (end < s[i].getLength())\r
{\r
- out.append(seq.substring(start, end) + "\n");\r
+ out.append(s[i].getSequence(start, end) + "\n");\r
}\r
- else if (start < seq.length())\r
+ else if (start < s[i].getLength())\r
{\r
- out.append(seq.substring(start) + "\n");\r
+ out.append(s[i].getSequence(start, s[i].getLength()) + "\n");\r
}\r
}\r
\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class FormatAdapter\r
+public class FormatAdapter extends AppletFormatAdapter\r
{\r
- /** DOCUMENT ME!! */\r
- public static final Vector formats = new Vector();\r
-\r
- static\r
- {\r
- formats.addElement("FASTA");\r
- formats.addElement("MSF");\r
- formats.addElement("PileUp");\r
- formats.addElement("CLUSTAL");\r
- formats.addElement("BLC");\r
- formats.addElement("PIR");\r
- formats.addElement("PFAM");\r
- }\r
-\r
- AlignFile afile = null;\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param inFile DOCUMENT ME!\r
- * @param type DOCUMENT ME!\r
- * @param format DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceI[] readFile(String inFile, String type, String format)\r
- {\r
- try\r
- {\r
- if (format.equals("FASTA"))\r
- {\r
- afile = new FastaFile(inFile, type);\r
- }\r
- else if (format.equals("MSF"))\r
- {\r
- afile = new MSFfile(inFile, type);\r
- }\r
- else if (format.equals("PileUp"))\r
- {\r
- afile = new PileUpfile(inFile, type);\r
- }\r
- else if (format.equals("CLUSTAL"))\r
- {\r
- afile = new ClustalFile(inFile, type);\r
- }\r
- else if (format.equals("BLC"))\r
- {\r
- afile = new BLCFile(inFile, type);\r
- }\r
- else if (format.equals("PIR"))\r
- {\r
- afile = new PIRFile(inFile, type);\r
- }\r
- else if (format.equals("PFAM"))\r
- {\r
- afile = new PfamFile(inFile, type);\r
- }\r
-\r
- return afile.getSeqsAsArray();\r
- }\r
- catch (Exception e)\r
- {\r
- System.err.println("Failed to read alignment using the '" + format +\r
- "' reader.");\r
- e.printStackTrace();\r
- }\r
-\r
- return null;\r
- }\r
-\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
if (format.equalsIgnoreCase("FASTA"))\r
{\r
afile = new FastaFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("MSF"))\r
{\r
- afile = new MSFfile();\r
+ afile = new MSFfile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("PileUp"))\r
{\r
afile = new PileUpfile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("CLUSTAL"))\r
{\r
afile = new ClustalFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("BLC"))\r
{\r
afile = new BLCFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("PIR"))\r
{\r
afile = new PIRFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));\r
}\r
else if (format.equalsIgnoreCase("PFAM"))\r
{\r
afile = new PfamFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));\r
}\r
\r
afile.setSeqs(s);\r
\r
import jalview.datamodel.*;\r
import jalview.gui.*;\r
-import jalview.schemes.*;\r
\r
public class HTMLOutput\r
{\r
AlignViewport av;\r
SequenceRenderer sr;\r
+ FeatureRenderer fr;\r
Color color;\r
\r
- public HTMLOutput(AlignViewport av)\r
+ public HTMLOutput(AlignViewport av, SequenceRenderer sr, FeatureRenderer fr)\r
{\r
this.av = av;\r
- sr = new SequenceRenderer(av);\r
+ this.sr = sr;\r
+ this.fr = fr;\r
\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
getProperty(\r
"<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\">\n");\r
\r
//////////////\r
- SequenceGroup[] groups;\r
SequenceI seq;\r
- ColourSchemeI cs = null;\r
AlignmentI alignment = av.getAlignment();\r
\r
// draws the top row, the measure rule\r
for (i = 0; i < alignment.getHeight(); i++)\r
{\r
seq = alignment.getSequenceAt(i);\r
- groups = alignment.findAllGroups(seq);\r
\r
- if (av.getShowFullId())\r
- {\r
- out.println("<tr><td nowrap>" + seq.getDisplayId() +\r
- " </td>");\r
- }\r
- else\r
- {\r
- out.println("<tr><td nowrap>" + seq.getName() +\r
+ String id = seq.getDisplayId(av.getShowJVSuffix());\r
+\r
+ out.println("<tr><td nowrap>" + id +\r
" </td>");\r
- }\r
+\r
\r
for (int res = 0; res < seq.getLength(); res++)\r
{\r
- cs = av.getGlobalColourScheme();\r
-\r
- if (groups != null)\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))\r
{\r
- for (int k = 0; k < groups.length; k++)\r
- {\r
- if ( (groups[k].getStartRes() <= res) &&\r
- (groups[k].getEndRes() >= res))\r
- {\r
- cs = groups[k].cs;\r
+ color = sr.getResidueBoxColour(seq, res);\r
\r
- break;\r
- }\r
- }\r
+ color = fr.findFeatureColour(color, seq, res);\r
}\r
+ else\r
+ color = Color.white;\r
\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
\r
- if (color.getRGB() < -1)\r
+ if (color.getRGB() < -1)\r
{\r
out.println("<td bgcolor=\"#" +\r
jalview.util.Format.getHexString(color) + "\">" +\r
////////////////////////////////////\r
/// How many sequences and residues can we fit on a printable page?\r
AlignmentI al = av.getAlignment();\r
- SequenceGroup[] groups;\r
SequenceI seq;\r
- ColourSchemeI cs = null;\r
String r;\r
String g;\r
String b;\r
endRes = al.getWidth();\r
}\r
\r
- out.println("<tr>");\r
- out.println("<td colspan=\"6\"> </td>");\r
-\r
- for (int i = startRes + 10; i < endRes; i += 10)\r
+ if(av.getScaleAboveWrapped())\r
{\r
- out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
- }\r
+ out.println("<tr>");\r
\r
- // out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
- // "<br>|</td>");\r
- out.println("</tr>");\r
+ if (av.getScaleLeftWrapped())\r
+ out.println("<td colspan=\"7\"> </td>");\r
+ else\r
+ out.println("<td colspan=\"6\"> </td>");\r
+\r
+\r
+ for (int i = startRes + 10; i < endRes; i += 10)\r
+ {\r
+ out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
+ }\r
+\r
+ out.println("</tr>");\r
+ }\r
\r
+ int startPos, endPos;\r
for (int s = 0; s < al.getHeight(); s++)\r
{\r
out.println("<tr>");\r
seq = al.getSequenceAt(s);\r
- groups = al.findAllGroups(seq);\r
\r
- if (av.getShowFullId())\r
- {\r
- out.println("<td nowrap>" + seq.getDisplayId() +\r
+ startPos = seq.findPosition( startRes );\r
+ endPos = seq.findPosition( endRes )-1;\r
+\r
+ String id = seq.getDisplayId(av.getShowJVSuffix());\r
+\r
+ out.println("<td nowrap>" + id +\r
" </td>");\r
- }\r
- else\r
+\r
+\r
+ if(av.getScaleLeftWrapped())\r
{\r
- out.println("<td nowrap>" + seq.getName() +\r
+ if(startPos > seq.getEnd() || endPos==0)\r
+ out.println("<td nowrap> </td>");\r
+ else\r
+ out.println("<td nowrap>" + startPos +\r
" </td>");\r
}\r
\r
+\r
for (int res = startRes; res < endRes; res++)\r
{\r
- cs = av.getGlobalColourScheme();\r
-\r
- if (groups != null)\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))\r
{\r
- for (int k = 0; k < groups.length; k++)\r
- {\r
- if ( (groups[k].getStartRes() <= res) &&\r
- (groups[k].getEndRes() >= res))\r
- {\r
- cs = groups[k].cs;\r
+ color = sr.getResidueBoxColour(seq, res);\r
\r
- break;\r
- }\r
- }\r
+ color = fr.findFeatureColour(color, seq, res);\r
}\r
-\r
- color = sr.getResidueBoxColour(cs, seq, res);\r
+ else\r
+ color = Color.white;\r
\r
if (color.getRGB() < -1)\r
{\r
{\r
out.println("<td>" + seq.getCharAt(res) + "</td>");\r
}\r
+\r
+\r
+ }\r
+\r
+ if(av.getScaleRightWrapped() &&\r
+ endRes < startRes + av.getWrappedWidth())\r
+ {\r
+ out.println("<td colspan=\""+ (startRes+av.getWrappedWidth()-endRes) +"\">"\r
+ +" </td>");\r
+ }\r
+\r
+\r
+ if(av.getScaleRightWrapped() && startPos<endPos)\r
+ {\r
+ out.println("<td nowrap> " + endPos +\r
+ " </td>");\r
}\r
\r
+\r
out.println("</tr>");\r
}\r
\r
// could be BLC file, read next line to confirm\r
data = reader.readLine();\r
\r
- if (data.indexOf(">") > -1)\r
+ if (data.indexOf(">") > -1 || data.indexOf("*") >-1 )\r
{\r
reply = "BLC";\r
}\r
maxLength = head.length();\r
}\r
\r
- if (head.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- head = st.nextToken();\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- }\r
-\r
-\r
// Replace ~ with a sensible gap character\r
seq = seq.replace('~', '-');\r
\r
- Sequence newSeq = new Sequence(head, seq, start, end);\r
+ Sequence newSeq = parseId(head);\r
+ newSeq.setSequence(seq);\r
\r
seqs.addElement(newSeq);\r
}\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static int checkSum(String seq)\r
+ public int checkSum(String seq)\r
{\r
int check = 0;\r
String sequence = seq.toUpperCase();\r
return check % 10000;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static String print(SequenceI[] s)\r
- {\r
- return print(s, false);\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public static String print(SequenceI[] seqs, boolean is_NA)\r
+ public String print(SequenceI[] seqs)\r
{\r
\r
+ boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);\r
+\r
SequenceI [] s = new SequenceI[seqs.length];\r
\r
StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +\r
{\r
if (sb.charAt(ii) == '.')\r
{\r
- sb.replace(ii, ii + 1, "~");\r
+ sb.setCharAt(ii, '~');\r
}\r
else\r
break;\r
{\r
if (sb.charAt(ii) == '.')\r
{\r
- sb.replace(ii, ii + 1, "~");\r
+ sb.setCharAt(ii,'~');\r
}\r
else\r
break;\r
while ((i < s.length) && (s[i] != null))\r
{\r
\r
- nameBlock[i] = new String(" Name: " + s[i].getName()\r
- + "/" + s[i].getStart() + "-" + s[i].getEnd()\r
- +" ");\r
+ nameBlock[i] = new String(" Name: " + printId(s[i])+" ");\r
\r
idBlock[i] = new String("Len: " +\r
maxLenpad.form(s[i].getSequence().length()) + " Check: " +\r
\r
while ((j < s.length) && (s[j] != null))\r
{\r
- String name = s[j].getName();\r
- // out.append(new Format("%-" + maxid + "s").form(name)+ " ");\r
+ String name = printId( s[j] );\r
\r
- out.append(new Format("%-" + maxid + "s").form(name\r
- + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+ out.append(new Format("%-" + maxid + "s").form(name+" "));\r
\r
\r
for (int k = 0; k < 5; k++)\r
{\r
try\r
{\r
- String id;\r
- String start;\r
- String end;\r
StringBuffer sequence;\r
String line = null;\r
\r
continue;\r
}\r
\r
- id = "No id";\r
- start = "1";\r
- end = "-1";\r
-\r
- try\r
- {\r
- int slashIndex = line.indexOf("/");\r
- if(slashIndex!=-1)\r
- {\r
- id = line.substring(line.indexOf(";") + 1, line.indexOf("/"));\r
- line = line.substring(line.indexOf("/") + 1);\r
- start = line.substring(0, line.indexOf("-"));\r
- end = line.substring(line.indexOf("-") + 1);\r
- }\r
- else\r
- {\r
- id = line.substring(line.indexOf(";")+1);\r
- }\r
- }\r
- catch (Exception ex)\r
- { }// Default id, start and end unchanged\r
+ Sequence newSeq = parseId(line.substring(line.indexOf(";") + 1));\r
\r
sequence = new StringBuffer();\r
\r
- line = nextLine(); // this is the title line\r
+ newSeq.setDescription(nextLine()); // this is the title line\r
\r
boolean starFound = false;\r
\r
{\r
sequence.setLength(sequence.length() - 1);\r
\r
- Sequence newSeq = new Sequence(id, sequence.toString(),\r
- Integer.parseInt(start),\r
- Integer.parseInt(end));\r
+ newSeq.setSequence(sequence.toString());\r
seqs.addElement(newSeq);\r
}\r
}\r
return print(getSeqsAsArray());\r
}\r
\r
- public static String print(SequenceI[] s)\r
- {\r
- return print(s, 72, true);\r
- }\r
-\r
- public static String print(SequenceI[] s, int len)\r
- {\r
- return print(s, len, true);\r
- }\r
-\r
- public static String print(SequenceI[] s, int len, boolean gaps)\r
+ public String print(SequenceI[] s)\r
{\r
+ boolean is_NA = jalview.util.Comparison.isNucleotide(s);\r
+ int len = 72;\r
StringBuffer out = new StringBuffer();\r
int i = 0;\r
\r
while ( (i < s.length) && (s[i] != null))\r
{\r
- String seq = "";\r
+ String seq = s[i].getSequence();\r
+ seq = seq + "*";\r
\r
- if (gaps)\r
- {\r
- seq = s[i].getSequence() + "*";\r
- }\r
+ out.append(">P1;" + printId(s[i]) + "\n");\r
+\r
+ if(s[i].getDescription()!=null)\r
+ out.append(s[i].getDescription()+"\n");\r
else\r
{\r
- seq = AlignSeq.extractGaps(s[i].getSequence(), "-");\r
- seq = AlignSeq.extractGaps(seq, ".");\r
- seq = AlignSeq.extractGaps(seq, " ");\r
- seq = seq + "*";\r
+ out.append(s[i].getName()+" "+ (s[i].getEnd() - s[i].getStart() + 1));\r
+ out.append( is_NA ? " bases\n" : " residues\n");\r
}\r
-\r
- out.append(">P1;" + s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd() + "\n");\r
- out.append(" Dummy title\n");\r
-\r
int nochunks = (seq.length() / len) + 1;\r
\r
for (int j = 0; j < nochunks; j++)\r
public class PfamFile\r
extends AlignFile\r
{\r
- Vector ids;\r
\r
public PfamFile()\r
{\r
public void initData()\r
{\r
super.initData();\r
- ids = new Vector();\r
}\r
\r
public void parse()\r
.length();\r
}\r
\r
- String head = headers.elementAt(i).toString();\r
- int start = 1;\r
- int end = -1;\r
\r
- if (head.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- ids.addElement(st.nextToken());\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- else\r
- {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
- }\r
- else\r
- {\r
- ids.addElement(headers.elementAt(i));\r
- }\r
-\r
- Sequence newSeq = null;\r
-\r
- newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqhash.get(headers.elementAt(i).toString())\r
- .toString(), start, end);\r
+ Sequence newSeq = parseId(headers.elementAt(i).toString());\r
+ newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString());\r
seqs.addElement(newSeq);\r
\r
-\r
if (!isValidProteinSequence(newSeq.getSequence()))\r
{\r
throw new IOException(\r
}\r
}\r
\r
- public static String print(SequenceI[] s)\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer("");\r
\r
\r
while ( (i < s.length) && (s[i] != null))\r
{\r
- String tmp = s[i].getName() + "/" + s[i].getStart() + "-" +\r
- s[i].getEnd();\r
+ String tmp = printId(s[i]);\r
\r
if (s[i].getSequence().length() > max)\r
{\r
\r
while ( (j < s.length) && (s[j] != null))\r
{\r
- out.append(new Format("%-" + maxid + "s").form(s[j].getName() +\r
- "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+ out.append(new Format("%-" + maxid + "s").form( printId(s[j])+" "));\r
\r
out.append(s[j].getSequence() + "\n");\r
j++;\r
*\r
**/\r
import java.io.*;\r
-import java.util.*;\r
\r
import jalview.datamodel.*;\r
import jalview.util.*;\r
\r
-public class PileUpfile\r
- extends AlignFile\r
+public class PileUpfile extends MSFfile\r
{\r
- public PileUpfile()\r
- {\r
- }\r
-\r
- public PileUpfile(String inStr)\r
- {\r
- super(inStr);\r
- }\r
\r
- public PileUpfile(String inFile, String type)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- public void parse()\r
- {\r
- int i = 0;\r
- boolean seqFlag = false;\r
- String key = new String();\r
- Vector headers = new Vector();\r
- Hashtable seqhash = new Hashtable();\r
- String line;\r
-\r
- try\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ */\r
+ public PileUpfile()\r
{\r
- while ( (line = nextLine()) != null)\r
- {\r
- StringTokenizer str = new StringTokenizer(line);\r
-\r
- while (str.hasMoreTokens())\r
- {\r
- String inStr = str.nextToken();\r
-\r
- //If line has header information add to the headers vector\r
- if (inStr.indexOf("Name:") != -1)\r
- {\r
- key = str.nextToken();\r
- headers.addElement(key);\r
- }\r
-\r
- //if line has // set SeqFlag to 1 so we know sequences are coming\r
- if (inStr.indexOf("//") != -1)\r
- {\r
- seqFlag = true;\r
- }\r
-\r
- //Process lines as sequence lines if seqFlag is set\r
- if ( (inStr.indexOf("//") == -1) && (seqFlag == true))\r
- {\r
- //seqeunce id is the first field\r
- key = inStr;\r
-\r
- StringBuffer tempseq;\r
-\r
- //Get sequence from hash if it exists\r
- if (seqhash.containsKey(key))\r
- {\r
- tempseq = (StringBuffer) seqhash.get(key);\r
- }\r
- else\r
- {\r
- tempseq = new StringBuffer();\r
- seqhash.put(key, tempseq);\r
- }\r
-\r
- //loop through the rest of the words\r
- while (str.hasMoreTokens())\r
- {\r
- //append the word to the sequence\r
- tempseq.append(str.nextToken());\r
- }\r
- }\r
- }\r
- }\r
}\r
- catch (IOException e)\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ *\r
+ * @param inStr DOCUMENT ME!\r
+ */\r
+ public PileUpfile(String inStr)\r
{\r
- System.err.println("Exception parsing PileUpfile " + e);\r
- e.printStackTrace();\r
+ super(inStr);\r
}\r
\r
- this.noSeqs = headers.size();\r
-\r
- //Add sequences to the hash\r
- for (i = 0; i < headers.size(); i++)\r
+ /**\r
+ * Creates a new MSFfile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public PileUpfile(String inFile, String type) throws IOException\r
{\r
- if (seqhash.get(headers.elementAt(i)) != null)\r
- {\r
- String head = headers.elementAt(i).toString();\r
- String seq = seqhash.get(head).toString();\r
-\r
- int start = 1;\r
- int end = -1;\r
-\r
- if (maxLength < head.length())\r
- {\r
- maxLength = head.length();\r
- }\r
-\r
- if (head.indexOf("/") > 0)\r
- {\r
- StringTokenizer st = new StringTokenizer(head, "/");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- head = st.nextToken();\r
-\r
- String tmp = st.nextToken();\r
- st = new StringTokenizer(tmp, "-");\r
-\r
- if (st.countTokens() == 2)\r
- {\r
- start = Integer.valueOf(st.nextToken()).intValue();\r
- end = Integer.valueOf(st.nextToken()).intValue();\r
- }\r
- }\r
- }\r
-\r
- Sequence newSeq = new Sequence(head, seq, start, end);\r
-\r
- seqs.addElement(newSeq);\r
- }\r
- else\r
- {\r
- System.err.println(\r
- "PileUpfile Parser: Can't find sequence for " +\r
- headers.elementAt(i));\r
- }\r
+ super(inFile, type);\r
}\r
- }\r
-\r
- public static int checkSum(String seq)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print()\r
{\r
-\r
- int check = 0;\r
-\r
- String sequence = seq.toUpperCase();\r
-\r
- for (int i = 0; i < sequence.length(); i++)\r
- {\r
- if (i < sequence.length())\r
- {\r
- int value = sequence.charAt(i);\r
- if (value != -1)\r
- {\r
- check += (i % 57 + 1) * value;\r
- }\r
- }\r
-\r
- }\r
-\r
- return check % 10000;\r
+ return print(getSeqsAsArray());\r
}\r
\r
- public static String print(SequenceI[] s)\r
+\r
+ public String print(SequenceI[] s)\r
{\r
StringBuffer out = new StringBuffer("PileUp\n\n");\r
\r
while ( (i < s.length) && (s[i] != null))\r
{\r
String seq = s[i].getSequence();\r
- out.append(" Name: " + s[i].getName() +\r
- "/" + s[i].getStart() + "-" + s[i].getEnd() +\r
+ out.append(" Name: " + printId(s[i]) +\r
" oo Len: " +\r
s[i].getSequence().length() + " Check: " + checksums[i] +\r
" Weight: 1.00\n");\r
\r
while ( (j < s.length) && (s[j] != null))\r
{\r
- String name = s[j].getName();\r
- // out.append(new Format("%-" + maxid + "s").form(name) + " ");\r
+ String name = printId(s[j]);\r
\r
- out.append(new Format("%-" + maxid + "s").form(name\r
- + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");\r
+ out.append(new Format("%-" + maxid + "s").form(name + " "));\r
\r
for (int k = 0; k < 5; k++)\r
{\r
\r
return out.toString();\r
}\r
-\r
- public String print()\r
- {\r
- return print(getSeqsAsArray());\r
- }\r
}\r
\r
import java.util.*;\r
\r
+import org.exolab.castor.mapping.Mapping;\r
+\r
+import org.exolab.castor.xml.*;\r
+import jalview.analysis.AlignSeq;\r
+\r
+\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public class SequenceFeatureFetcher implements Runnable\r
{\r
- AlignmentI align;\r
- AlignmentPanel ap;\r
- ArrayList unknownSequences;\r
- CutAndPasteTransfer output = new CutAndPasteTransfer();\r
- StringBuffer sbuffer = new StringBuffer();\r
-\r
- /**\r
- * Creates a new SequenceFeatureFetcher object.\r
- *\r
- * @param align DOCUMENT ME!\r
- * @param ap DOCUMENT ME!\r
- */\r
- public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
- {\r
- unknownSequences = new ArrayList();\r
- this.align = align;\r
- this.ap = ap;\r
-\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
- {\r
- RandomAccessFile out = null;\r
-\r
- try\r
- {\r
- String cache = System.getProperty("user.home") +\r
- "/.jalview.uniprot.xml";\r
-\r
- File test = new File(cache);\r
-\r
- if (!test.exists())\r
- {\r
- out = new RandomAccessFile(cache, "rw");\r
- out.writeBytes("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");\r
- out.writeBytes("<UNIPROT_CACHE>\n");\r
- }\r
- else\r
- {\r
- out = new RandomAccessFile(cache, "rw");\r
-\r
- // open exisiting cache and remove </UNIPROT_CACHE> from the end\r
- long lastLine = 0;\r
- String data;\r
-\r
- while ((data = out.readLine()) != null)\r
- {\r
- if (data.indexOf("</entry>") > -1)\r
- {\r
- lastLine = out.getFilePointer();\r
- }\r
- }\r
-\r
- out.seek(lastLine);\r
- }\r
-\r
- int seqIndex = 0;\r
- Vector sequences = align.getSequences();\r
\r
- while (seqIndex < sequences.size())\r
- {\r
- ArrayList ids = new ArrayList();\r
+ AlignmentI align;\r
+ AlignmentI dataset;\r
+ AlignmentPanel ap;\r
+ ArrayList unknownSequences;\r
+ CutAndPasteTransfer output = new CutAndPasteTransfer();\r
+ StringBuffer sbuffer = new StringBuffer();\r
+ boolean uniprotFlag = false;\r
\r
- for (int i = 0; (seqIndex < sequences.size()) && (i < 50);\r
- seqIndex++, i++)\r
- {\r
- SequenceI sequence = (SequenceI) sequences.get(seqIndex);\r
- ids.add(sequence.getName());\r
- }\r
+ public SequenceFeatureFetcher()\r
+ {}\r
\r
- tryLocalCacheFirst(ids, align);\r
+ public Vector getUniprotEntries(File file)\r
+ {\r
\r
- if (ids.size() > 0)\r
- {\r
- StringBuffer remainingIds = new StringBuffer("uniprot:");\r
+ UniprotFile uni = new UniprotFile();\r
+ try\r
+ {\r
+ // 1. Load the mapping information from the file\r
+ Mapping map = new Mapping(uni.getClass().getClassLoader());\r
+ java.net.URL url = getClass().getResource("/uniprot_mapping.xml");\r
+ map.loadMapping(url);\r
\r
- for (int i = 0; i < ids.size(); i++)\r
- remainingIds.append(ids.get(i) + ";");\r
+ // 2. Unmarshal the data\r
+ Unmarshaller unmar = new Unmarshaller();\r
+ unmar.setIgnoreExtraElements(true);\r
+ unmar.setMapping(map);\r
+ uni = (UniprotFile) unmar.unmarshal(new FileReader(file));\r
\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData(remainingIds.toString(),\r
- "xml", null);\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ System.out.println("Error getUniprotEntries() "+e);\r
+ }\r
+ return uni.getUniprotEntries();\r
+ }\r
+\r
+ /**\r
+ * Creates a new SequenceFeatureFetcher object.\r
+ *\r
+ * @param align DOCUMENT ME!\r
+ * @param ap DOCUMENT ME!\r
+ */\r
+ public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
+ {\r
+ unknownSequences = new ArrayList();\r
+ this.align = align;\r
+ this.dataset = align.getDataset();\r
+ this.ap = ap;\r
+\r
+ Thread thread = new Thread(this);\r
+ thread.start();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ int seqIndex = 0;\r
+ Vector sequences = dataset.getSequences();\r
\r
- if (result != null)\r
- {\r
- ReadUniprotFile(result, out, align);\r
- }\r
- }\r
- }\r
+ while (seqIndex < sequences.size())\r
+ {\r
+ Vector ids = new Vector();\r
\r
- if (out != null)\r
+ for (int i = 0; (seqIndex < sequences.size()) && (i < 50);\r
+ seqIndex++, i++)\r
+ {\r
+ Sequence sequence = (Sequence) sequences.get(seqIndex);\r
+ if(sequence.getSequenceFeatures()==null)\r
+ {\r
+ if (!ids.contains(sequence.getName()))\r
{\r
- out.writeBytes("</UNIPROT_CACHE>\n");\r
- out.close();\r
+ ids.add(sequence.getName());\r
+ unknownSequences.add(sequence);\r
}\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
+ }\r
}\r
\r
- findMissingIds(align);\r
-\r
- if (sbuffer.length() > 0)\r
+ ///////////////////////////////////\r
+ ///READ FROM EBI\r
+ if (ids.size() > 0)\r
{\r
- output.setText(\r
- "Your sequences have been matched to Uniprot. Some of the ids have been\n" +\r
- "altered, most likely the start/end residue will have been updated.\n" +\r
- "Save your alignment to maintain the updated id.\n\n" +\r
- sbuffer.toString());\r
- Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
+ StringBuffer remainingIds = new StringBuffer("uniprot:");\r
+ for (int i = 0; i < ids.size(); i++)\r
+ {\r
+ if(ids.get(i).toString().indexOf("|")>-1)\r
+ {\r
+ remainingIds.append(ids.get(i).toString().substring(\r
+ ids.get(i).toString().lastIndexOf("|") + 1));\r
+ uniprotFlag = true;\r
+ }\r
+ remainingIds.append(ids.get(i) + ";");\r
+ }\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ File file = ebi.fetchDataAsFile(remainingIds.toString(),\r
+ "xml", "raw");\r
+\r
+\r
+\r
+ if (file != null)\r
+ {\r
+ ReadUniprotFile(file, ids);\r
+ }\r
}\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
\r
- if (unknownSequences.size() > 0)\r
- {\r
- //ignore for now!!!!!!!!!!\r
- // WSWUBlastClient blastClient = new WSWUBlastClient(align, unknownSequences);\r
- }\r
+ if (sbuffer.length() > 0)\r
+ {\r
+ output.setText(\r
+ "Your sequences have been matched to Uniprot. Some of the ids have been\n" +\r
+ "altered, most likely the start/end residue will have been updated.\n" +\r
+ "Save your alignment to maintain the updated id.\n\n" +\r
+ sbuffer.toString());\r
+ Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
+ // The above is the dataset, we must now find out the index\r
+ // of the viewed sequence\r
\r
- jalview.gui.PaintRefresher.Refresh(null, align);\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param result DOCUMENT ME!\r
- * @param out DOCUMENT ME!\r
- * @param align DOCUMENT ME!\r
- */\r
- void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align)\r
- {\r
- SequenceI sequence = null;\r
- Vector features = null;\r
- String type;\r
- String description;\r
- String status;\r
- String start;\r
- String end;\r
- String pdb = null;\r
-\r
- for (int r = 0; r < result.length; r++)\r
- {\r
- if ((sequence == null) && (result[r].indexOf("<name>") > -1))\r
- {\r
- long filePointer = 0;\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- filePointer = out.getFilePointer();\r
- out.writeBytes("<entry>\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- String seqName = parseElement(result[r], "<name>", out);\r
- sequence = align.findName(seqName);\r
-\r
- if (sequence == null)\r
- {\r
- sequence = align.findName(seqName.substring(0,\r
- seqName.indexOf('_')));\r
-\r
- if (sequence != null)\r
- {\r
- sbuffer.append("changing " + sequence.getName() +\r
- " to " + seqName + "\n");\r
- sequence.setName(seqName);\r
- }\r
- }\r
-\r
- if (sequence == null)\r
- {\r
- sbuffer.append("UNIPROT updated suggestion is " +\r
- result[r] + "\n");\r
- sequence = align.findName(result[r]);\r
-\r
- // this entry has been suggested by ebi.\r
- // doesn't match id in alignment file\r
- try\r
- {\r
- out.setLength(filePointer);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- // now skip to next entry\r
- while (result[r].indexOf("</entry>") == -1)\r
- r++;\r
- }\r
-\r
- features = new Vector();\r
- type = "";\r
- start = "0";\r
- end = "0";\r
- description = "";\r
- status = "";\r
- pdb = "";\r
- }\r
+ promptBeforeBlast();\r
\r
- if (sequence == null)\r
- {\r
- continue;\r
- }\r
+ }\r
\r
- if (result[r].indexOf("<property type=\"pdb accession\"") > -1)\r
- {\r
- pdb = parseValue(result[r], "value=", out);\r
- sequence.setPDBId(pdb);\r
- }\r
\r
- if (result[r].indexOf("feature type") > -1)\r
- {\r
- type = parseValue(result[r], "type=", out);\r
- description = parseValue(result[r], "description=", null);\r
- status = parseValue(result[r], "status=", null);\r
-\r
- while (result[r].indexOf("position") == -1)\r
- {\r
- r++; //<location>\r
- }\r
-\r
- // r++;\r
- if (result[r].indexOf("begin") > -1)\r
- {\r
- start = parseValue(result[r], "position=", out);\r
- end = parseValue(result[++r], "position=", out);\r
- }\r
- else\r
- {\r
- start = parseValue(result[r], "position=", out);\r
- end = parseValue(result[r], "position=", null);\r
- }\r
-\r
- int sstart = Integer.parseInt(start);\r
- int eend = Integer.parseInt(end);\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes("</feature>\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- SequenceFeature sf = new SequenceFeature(type, sstart, eend,\r
- description, status);\r
- features.add(sf);\r
- }\r
+ void promptBeforeBlast()\r
+ {\r
+ // This must be outside the run() body as java 1.5\r
+ // will not return any value from the OptionPane to the expired thread.\r
+ if (unknownSequences.size() > 0)\r
+ {\r
+ int reply = javax.swing.JOptionPane.showConfirmDialog(\r
+ Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences."\r
+ +"\nPerform blast for unknown sequences?",\r
+ "Blast for Unidentified Sequences",\r
+ javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);\r
\r
- if (result[r].indexOf("<sequence length=") > -1)\r
- {\r
- StringBuffer seqString = new StringBuffer();\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes(result[r] + "\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- while (result[++r].indexOf("</sequence>") == -1)\r
- {\r
- seqString.append(result[r]);\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes(result[r] + "\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
- }\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes(result[r] + "\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- StringBuffer nonGapped = new StringBuffer();\r
-\r
- for (int i = 0; i < sequence.getSequence().length(); i++)\r
- {\r
- if (!jalview.util.Comparison.isGap(sequence.getCharAt(i)))\r
- {\r
- nonGapped.append(sequence.getCharAt(i));\r
- }\r
- }\r
-\r
- int absStart = seqString.toString().indexOf(nonGapped.toString());\r
-\r
- if (absStart == -1)\r
- {\r
- unknownSequences.add(sequence.getName());\r
- features = null;\r
- sbuffer.append(sequence.getName() +\r
- " SEQUENCE NOT %100 MATCH \n");\r
-\r
- continue;\r
- }\r
-\r
- int absEnd = absStart + nonGapped.toString().length();\r
- absStart += 1;\r
-\r
- if ((absStart != sequence.getStart()) ||\r
- (absEnd != sequence.getEnd()))\r
- {\r
- sbuffer.append("Updated: " + sequence.getName() + " " +\r
- sequence.getStart() + "/" + sequence.getEnd() +\r
- " to " + absStart + "/" + absEnd + "\n");\r
- }\r
-\r
- sequence.setStart(absStart);\r
- sequence.setEnd(absEnd);\r
- }\r
+ if(reply == javax.swing.JOptionPane.YES_OPTION)\r
+ new WSWUBlastClient(ap, align, unknownSequences);\r
+ }\r
\r
- if (result[r].indexOf("</entry>") > -1)\r
- {\r
- if (features != null)\r
- {\r
- sequence.setSequenceFeatures(features);\r
- }\r
-\r
- features = null;\r
- sequence = null;\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes("</entry>\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
- }\r
- }\r
- }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param align DOCUMENT ME!\r
- */\r
- void findMissingIds(AlignmentI align)\r
- {\r
- String data;\r
- ArrayList cachedIds = new ArrayList();\r
+ ap.repaint();\r
+ }\r
\r
- try\r
- {\r
- if(jalview.bin.Cache.getProperty("UNIPROT_CACHE")==null)\r
- return;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param result DOCUMENT ME!\r
+ * @param out DOCUMENT ME!\r
+ * @param align DOCUMENT ME!\r
+ */\r
+ void ReadUniprotFile(File file, Vector ids)\r
+ {\r
+ if(!file.exists())\r
+ return;\r
\r
- BufferedReader in = new BufferedReader(new FileReader(\r
- jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
+ SequenceI sequence = null;\r
\r
- while ((data = in.readLine()) != null)\r
- {\r
- if (data.indexOf("name") > -1)\r
- {\r
- String name = parseElement(data, "<name>", null);\r
- cachedIds.add(name);\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
+ Vector entries = getUniprotEntries(file);\r
+\r
+ int i, iSize = entries==null?0:entries.size();\r
+ UniprotEntry entry;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ entry = (UniprotEntry) entries.elementAt(i);\r
+ String idmatch = entry.getAccession().elementAt(0).toString();\r
+ sequence = dataset.findName(idmatch);\r
+\r
+ if (sequence == null)\r
+ {\r
+ //Sequence maybe Name, not Accession\r
+ idmatch = entry.getName().elementAt(0).toString();\r
+ sequence = dataset.findName(idmatch);\r
+ }\r
+\r
+ if(sequence!=null)\r
+ ids.remove(sequence.getName());\r
+\r
+ else if (sequence == null && uniprotFlag)\r
+ {\r
+ sequence = dataset.findName("UniProt/Swiss-Prot|"+entry.getAccession().elementAt(0)+"|"+idmatch);\r
+ ids.remove(idmatch);\r
+ }\r
+\r
+ if(sequence ==null)\r
+ {\r
+ System.out.println(idmatch+" not found");\r
+ continue;\r
+ }\r
+\r
+ unknownSequences.remove(sequence);\r
+\r
+ String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());\r
+\r
+ int absStart = entry.getUniprotSequence().getContent().indexOf(\r
+ nonGapped.toString());\r
+\r
+ if (absStart == -1)\r
+ {\r
+ // Is UniprotSequence contained in dataset sequence?\r
+ absStart = nonGapped.toString().indexOf(entry.getUniprotSequence().getContent());\r
+ if(absStart == -1)\r
{\r
- ex.printStackTrace();\r
- }\r
+ unknownSequences.add(sequence.getName());\r
+ sbuffer.append(sequence.getName() +\r
+ " SEQUENCE NOT %100 MATCH \n");\r
\r
- for (int i = 0; i < align.getHeight(); i++)\r
- if (!cachedIds.contains(align.getSequenceAt(i).getName()))\r
+ continue;\r
+ }\r
+ else\r
+ {\r
+ if(entry.getFeature()!=null)\r
+ {\r
+ Enumeration e = entry.getFeature().elements();\r
+ while (e.hasMoreElements())\r
{\r
- unknownSequences.add(align.getSequenceAt(i).getName());\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ sf.setBegin(sf.getBegin() + absStart + 1);\r
+ sf.setEnd(sf.getEnd() + absStart + 1);\r
}\r
- }\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ids DOCUMENT ME!\r
- * @param align DOCUMENT ME!\r
- */\r
- void tryLocalCacheFirst(ArrayList ids, AlignmentI align)\r
- {\r
- ArrayList cacheData = new ArrayList();\r
+ sbuffer.append(sequence.getName() +\r
+ " HAS "+absStart+" PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"\r
+ +" HAVE BEEN ADJUSTED ACCORDINGLY \n");\r
+ absStart = 0;\r
+ }\r
\r
- try\r
- {\r
- if(jalview.bin.Cache.getProperty("UNIPROT_CACHE")==null)\r
- return;\r
+ }\r
\r
- BufferedReader in = new BufferedReader(new FileReader(\r
- jalview.bin.Cache.getProperty("UNIPROT_CACHE")));\r
+ int absEnd = absStart + nonGapped.toString().length();\r
+ absStart += 1;\r
\r
- // read through cache file, if the cache has sequences we're looking for\r
- // add the lines to a new String array, Readthis new array and\r
- // make sure we remove the ids from the list to retrieve from EBI\r
- String data;\r
+ Enumeration e = entry.getDbReference().elements();\r
+ Vector onlyPdbEntries = new Vector();\r
+ while(e.hasMoreElements())\r
+ {\r
+ PDBEntry pdb = (PDBEntry)e.nextElement();\r
+ if(!pdb.getType().equals("PDB"))\r
+ continue;\r
\r
- while ((data = in.readLine()) != null)\r
- {\r
- if (data.indexOf("name") > -1)\r
- {\r
- String name = parseElement(data, "<name>", null);\r
-\r
- if (ids.contains(name))\r
- {\r
- cacheData.add("<entry>");\r
- cacheData.add(data);\r
-\r
- while (data.indexOf("</entry>") == -1)\r
- {\r
- data = in.readLine();\r
- cacheData.add(data);\r
- }\r
-\r
- cacheData.add(data);\r
-\r
- ids.remove(name);\r
- }\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ onlyPdbEntries.addElement(pdb);\r
+ }\r
\r
- String[] localData = new String[cacheData.size()];\r
- cacheData.toArray(localData);\r
+ sequence.setPDBId(onlyPdbEntries);\r
+ sequence.setSequenceFeatures(entry.getFeature());\r
+ sequence.setStart(absStart);\r
+ sequence.setEnd(absEnd);\r
\r
- if ((localData != null) && (localData.length > 0))\r
- {\r
- ReadUniprotFile(localData, null, align);\r
- }\r
- }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param line DOCUMENT ME!\r
- * @param tag DOCUMENT ME!\r
- * @param out DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- String parseValue(String line, String tag, RandomAccessFile out)\r
- {\r
- if (out != null)\r
+ int n = 0;\r
+ SequenceI seq2;\r
+ while (n < align.getHeight())\r
+ {\r
+ //This loop enables multiple sequences with the same\r
+ //id to have features added and seq limits updated\r
+ seq2 = align.getSequenceAt(n);\r
+ if (seq2.getName().equals(idmatch))\r
{\r
- try\r
- {\r
- out.writeBytes(line + "\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
\r
- int index = line.indexOf(tag) + tag.length() + 1;\r
+ nonGapped = AlignSeq.extractGaps("-. ", seq2.getSequence());\r
\r
- if (index == tag.length())\r
- {\r
- return "";\r
- }\r
+ absStart = sequence.getSequence().indexOf(nonGapped);\r
+ absEnd = absStart + nonGapped.toString().length() - 1;\r
\r
- return line.substring(index, line.indexOf("\"", index + 1));\r
- }\r
+ // This is the Viewd alignment sequences\r
+ // No need to tell the user of the dataset updates\r
+ if ( (seq2.getStart() != absStart+sequence.getStart())\r
+ || (seq2.getEnd() != absEnd+sequence.getStart()))\r
+ {\r
+ sbuffer.append("Updated: " + seq2.getName() + " " +\r
+ seq2.getStart() + "/" + seq2.getEnd() +\r
+ " to " + (absStart + sequence.getStart()) + "/" +\r
+ (absEnd + sequence.getStart()) + "\n");\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param line DOCUMENT ME!\r
- * @param tag DOCUMENT ME!\r
- * @param out DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- String parseElement(String line, String tag, RandomAccessFile out)\r
- {\r
- if (out != null)\r
- {\r
- try\r
- {\r
- out.writeBytes(line + "\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
+ seq2.setStart(absStart + sequence.getStart());\r
+ seq2.setEnd(absEnd + sequence.getStart());\r
+ }\r
}\r
\r
- int index = line.indexOf(tag) + tag.length();\r
-\r
- return line.substring(index, line.indexOf("</"));\r
+ n++;\r
+ }\r
}\r
+ }\r
}\r
+\r
+\r
import javax.swing.*;\r
\r
import javax.xml.namespace.QName;\r
+import jalview.analysis.AlignSeq;\r
\r
+import uk.ac.ebi.www.*;\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public class WSWUBlastClient\r
{\r
+ AlignmentPanel ap;\r
+ AlignmentI al;\r
CutAndPasteTransfer output = new CutAndPasteTransfer();\r
int jobsRunning = 0;\r
\r
+ Vector suggestedIds = new Vector();\r
/**\r
* Creates a new WSWUBlastClient object.\r
*\r
* @param al DOCUMENT ME!\r
* @param ids DOCUMENT ME!\r
*/\r
- public WSWUBlastClient(AlignmentI al, ArrayList ids)\r
+ public WSWUBlastClient(AlignmentPanel ap, AlignmentI al, ArrayList ids)\r
{\r
+ this.ap = ap;\r
+ this.al = al;\r
output.setText(\r
- "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered." +\r
- "\nIn order to display these features, try changing the names of your sequences to the ids suggested below.");\r
+ "To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."\r
+ +"\nIn order to display these features, try changing the names of your sequences to the ids suggested below."\r
+ +"\n\nRunning WSWUBlast at EBI."\r
+ +"\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."\r
+ +"\nSOAP-based services provided by the European Bioinformatics Institute."\r
+ +"\nNucleic Acids Res. 33(1):W25-W28 (2005));");\r
+\r
Desktop.addInternalFrame(output,\r
"BLASTing for unidentified sequences ", 800, 300);\r
\r
for (int i = 0; i < ids.size(); i++)\r
{\r
- SequenceI sequence = al.findName(ids.get(i).toString());\r
- StringBuffer nonGapped = new StringBuffer();\r
-\r
- for (int n = 0; n < sequence.getSequence().length(); n++)\r
- {\r
- if (!jalview.util.Comparison.isGap(sequence.getCharAt(n)))\r
- {\r
- nonGapped.append(sequence.getCharAt(n));\r
- }\r
- }\r
+ Sequence sequence = (Sequence)ids.get(i);\r
+ System.out.println(sequence.getName());\r
\r
- BlastThread thread = new BlastThread(ids.get(i).toString(),\r
- nonGapped.toString());\r
+ BlastThread thread = new BlastThread(sequence);\r
thread.start();\r
jobsRunning++;\r
}\r
thread.start();\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @param id1 DOCUMENT ME!\r
* @param res DOCUMENT ME!\r
*/\r
- void parseResult(String id1, String res)\r
+ void parseResult(Sequence seq, String res)\r
{\r
StringTokenizer st = new StringTokenizer(res, "\n");\r
String data;\r
String id2;\r
int maxFound = 90;\r
- StringBuffer buffer = new StringBuffer("\n\n" + id1 + " :");\r
+ StringBuffer buffer = new StringBuffer("\n\n" + seq.getName() + " :");\r
\r
while (st.hasMoreTokens())\r
{\r
data = st.nextToken();\r
\r
- if (data.indexOf("database=\"uniprot\" id=") > -1)\r
+ if (data.indexOf(">UNIPROT") > -1)\r
{\r
- int index = data.indexOf("database=\"uniprot\" id=") + 23;\r
- id2 = data.substring(index, data.indexOf("\"", index));\r
+ int index = data.indexOf(">UNIPROT") + 9;\r
+ id2 = data.substring(index, data.indexOf(" ", index));\r
\r
- while (data.indexOf("</alignment>") == -1)\r
+ boolean identitiesFound = false;\r
+ while (!identitiesFound)\r
{\r
data = st.nextToken();\r
\r
- if (data.indexOf("<identity>") > -1)\r
+ if (data.indexOf("Identities") > -1)\r
{\r
- int value = Integer.parseInt(data.substring(data.indexOf(\r
- "<identity>") + 10,\r
- data.indexOf("</identity>")));\r
+ identitiesFound = true;\r
+\r
+ int value = Integer.parseInt(data.substring(data.indexOf(\r
+ "(") + 1,\r
+ data.indexOf("%")));\r
\r
if (value >= maxFound)\r
{\r
maxFound = value;\r
buffer.append(" " + id2 + " " + value + "%; ");\r
+ suggestedIds.addElement( new Object[]{seq, id2});\r
}\r
}\r
}\r
}\r
}\r
\r
- output.setText(output.getText() + buffer.toString());\r
+ output.appendText(buffer.toString());\r
+ }\r
+\r
+ void updateIds()\r
+ {\r
+ // This must be outside the run() body as java 1.5\r
+ // will not return any value from the OptionPane to the expired thread.\r
+ int reply = JOptionPane.showConfirmDialog(\r
+ Desktop.desktop, "Automatically update suggested ids?",\r
+ "Auto replace sequence ids", JOptionPane.YES_NO_OPTION);\r
+\r
+ if (reply == JOptionPane.YES_OPTION)\r
+ {\r
+ Enumeration keys = suggestedIds.elements();\r
+ while(keys.hasMoreElements())\r
+ {\r
+ Object [] object = (Object[])keys.nextElement();\r
+\r
+ Sequence oldseq = (Sequence)object[0];\r
+\r
+ oldseq.setName( object[1].toString() );\r
+\r
+ // Oldseq is actually in the dataset, we must find the\r
+ // Visible seq and change its name also.\r
+ for (int i = 0; i < al.getHeight(); i++)\r
+ {\r
+ if (al.getSequenceAt(i).getDatasetSequence() == oldseq)\r
+ {\r
+ al.getSequenceAt(i).setName(oldseq.getName());\r
+ break;\r
+ }\r
+ }\r
+\r
+ Vector entries = oldseq.getDBRef();\r
+ if (entries != null)\r
+ {\r
+ DBRefEntry entry = (DBRefEntry) entries.elementAt(0);\r
+ oldseq.addDBRef(new jalview.datamodel.\r
+ DBRefEntry("UNIPROT",\r
+ "0",\r
+ entry.getAccessionId()));\r
+ }\r
+ }\r
+ }\r
+ ap.repaint();\r
+\r
}\r
\r
class ImageTwirler extends Thread\r
{\r
}\r
}\r
+\r
+ if (jobsRunning == 0)\r
+ {\r
+ updateIds();\r
+ }\r
}\r
}\r
\r
class BlastThread extends Thread\r
{\r
- String sequence;\r
- String seqid;\r
+ Sequence sequence;\r
String jobid;\r
boolean jobComplete = false;\r
\r
- BlastThread(String id, String sequence)\r
+ BlastThread(Sequence sequence)\r
{\r
- this.sequence = sequence;\r
- seqid = id;\r
+ System.out.println("blasting for: "+sequence.getName());\r
+ this.sequence = sequence;\r
}\r
\r
public void run()\r
{\r
try\r
{\r
- Call call = (Call) new Service().createCall();\r
- call.setTargetEndpointAddress(new java.net.URL(\r
- "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
- call.setOperationName(new QName("WSWUBlast", "polljob"));\r
-\r
- String result = (String) call.invoke(new Object[]\r
- {\r
- jobid, "xml"\r
- });\r
-\r
- if ((result.indexOf("JOB PENDING") == -1) &&\r
- (result.indexOf("JOB RUNNING") == -1))\r
- {\r
- parseResult(seqid, result);\r
- jobComplete = true;\r
- jobsRunning--;\r
- }\r
-\r
- Thread.sleep(5000);\r
-\r
- // System.out.println("WSWuBlastClient: I'm alive "+seqid+" "+jobid); // log.debug\r
+ WSWUBlastService service = new WSWUBlastServiceLocator();\r
+ WSWUBlast wublast = service.getWSWUBlast();\r
+ WSFile[] results = wublast.getResults(jobid);\r
+\r
+ if(results!=null)\r
+ {\r
+ String result = new String(wublast.poll(jobid, "tooloutput"));\r
+ parseResult(sequence, result);\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ }\r
+ else\r
+ {\r
+ Thread.sleep(10000);\r
+ System.out.println("WSWuBlastClient: I'm alive " +\r
+ sequence.getName() + " " + jobid); // log.debug\r
+ }\r
}\r
catch (Exception ex)\r
{\r
\r
void StartJob()\r
{\r
- HashMap params = new HashMap();\r
- params.put("database", "uniprot");\r
- params.put("sensitivity", "low");\r
- params.put("sort", "totalscore");\r
- params.put("matrix", "pam10");\r
- params.put("program", "blastp");\r
- params.put("alignments", "5");\r
- params.put("outformat", "xml");\r
- params.put("searchtype", "1");\r
-\r
- byte[] seqbytes = sequence.getBytes();\r
+ InputParams params = new InputParams();\r
+\r
+ params.setProgram("blastp");\r
+ params.setDatabase("uniprot");\r
+ params.setMatrix("pam10");\r
+\r
+ params.setNumal(5);\r
+ params.setSensitivity("low");\r
+ params.setSort("totalscore");\r
+ params.setOutformat("txt");\r
+ params.setAsync(true);\r
\r
try\r
{\r
- Call call = (Call) new Service().createCall();\r
- call.setTargetEndpointAddress(new java.net.URL(\r
- "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast"));\r
- call.setOperationName(new QName("WSWUBlast", "doWUBlast"));\r
-\r
- String result = (String) call.invoke(new Object[]\r
- {\r
- params, seqbytes\r
- });\r
- jobid = result;\r
- System.out.println(\r
- "http://www.ebi.ac.uk/cgi-bin/webservices/WSWUBlast JobId '" +\r
- jobid + "'");\r
+ Data inputs[] = new Data[1];\r
+ Data input= new Data();\r
+ input.setType("sequence");\r
+ input.setContent(AlignSeq.extractGaps("-. ",sequence.getSequence()));\r
+ inputs[0]=input;\r
+\r
+ WSWUBlastService service = new WSWUBlastServiceLocator();\r
+ WSWUBlast wublast = service.getWSWUBlast();\r
+ jobid = wublast.runWUBlast(params, inputs);\r
}\r
catch (Exception exp)\r
{\r
- System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
- exp.printStackTrace();\r
+ jobComplete = true;\r
+ jobsRunning--;\r
+ System.err.println("WSWUBlastClient error:\n" + exp.toString());\r
+ exp.printStackTrace();\r
}\r
}\r
}\r
import java.awt.*;\r
import java.awt.event.*;\r
import javax.swing.*;\r
-import javax.swing.event.*;\r
\r
import jalview.schemes.*;\r
\r
public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
JMenuItem createPNG = new JMenuItem();\r
protected JMenuItem font = new JMenuItem();\r
- public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
+ public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
JMenuItem epsFile = new JMenuItem();\r
JMenuItem LoadtreeMenuItem = new JMenuItem();\r
public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
JMenu jMenu2 = new JMenu();\r
JMenuItem padGapsMenuitem = new JMenuItem();\r
protected ButtonGroup colours = new ButtonGroup();\r
+ JMenuItem vamsasStore = new JMenuItem();\r
+ protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
+ //protected JTabbedPane tabbedPane = new JTabbedPane();\r
+ public JMenuItem featureSettings = new JMenuItem();\r
+ JMenuItem fetchSequence = new JMenuItem();\r
\r
public GAlignFrame()\r
{\r
});\r
this.getContentPane().setLayout(borderLayout1);\r
alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
- {\r
- public void ancestorAdded(AncestorEvent event)\r
- {\r
- alignFrameMenuBar_ancestorAdded(event);\r
- }\r
-\r
- public void ancestorRemoved(AncestorEvent event)\r
- {\r
- }\r
-\r
- public void ancestorMoved(AncestorEvent event)\r
- {\r
- }\r
- });\r
statusBar.setBackground(Color.white);\r
statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
font_actionPerformed(e);\r
}\r
});\r
- fullSeqId.setText("Show Full Sequence ID");\r
- fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",true));\r
- fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
+\r
+ seqLimits.setText("Show Sequence Limits");\r
+ seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
+ seqLimits.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- fullSeqId_actionPerformed(e);\r
+ seqLimit_actionPerformed(e);\r
}\r
});\r
epsFile.setText("EPS");\r
padGapsMenuitem_actionPerformed(e);\r
}\r
});\r
+ vamsasStore.setVisible(false);\r
+ vamsasStore.setText("VAMSAS store");\r
+ vamsasStore.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ vamsasStore_actionPerformed(e);\r
+ }\r
+ });\r
+ showTranslation.setText("Translate cDNA");\r
+ showTranslation.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showTranslation_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ /* tabbedPane.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent ece)\r
+ {\r
+\r
+ tabSelected();\r
+ }\r
+ });*/\r
+ featureSettings.setEnabled(false);\r
+ featureSettings.setText("Feature Settings...");\r
+ featureSettings.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ featureSettings_actionPerformed(e);\r
+ }\r
+ });\r
+ fetchSequence.setText("Fetch Sequence...");\r
+ fetchSequence.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ fetchSequence_actionPerformed(e);\r
+ }\r
+ });\r
alignFrameMenuBar.add(fileMenu);\r
alignFrameMenuBar.add(editMenu);\r
alignFrameMenuBar.add(searchMenu);\r
alignFrameMenuBar.add(colourMenu);\r
alignFrameMenuBar.add(calculateMenu);\r
alignFrameMenuBar.add(webService);\r
+ fileMenu.add(fetchSequence);\r
+ fileMenu.add(vamsasStore);\r
fileMenu.add(saveAlignmentMenu);\r
fileMenu.add(jMenu2);\r
fileMenu.add(outputTextboxMenu);\r
viewMenu.add(font);\r
viewMenu.addSeparator();\r
viewMenu.add(wrapMenuItem);\r
- viewMenu.add(fullSeqId);\r
+ viewMenu.add(seqLimits);\r
viewMenu.add(scaleAbove);\r
viewMenu.add(scaleLeft);\r
viewMenu.add(scaleRight);\r
viewMenu.add(colourTextMenuItem);\r
viewMenu.add(renderGapsMenuItem);\r
viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
viewMenu.add(sequenceFeatures);\r
+ viewMenu.add(featureSettings);\r
viewMenu.addSeparator();\r
viewMenu.add(overviewMenuItem);\r
colourMenu.add(applyToAllGroups);\r
calculateMenu.addSeparator();\r
calculateMenu.add(pairwiseAlignmentMenuItem);\r
calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(showTranslation);\r
webServiceNoServices=new JMenuItem("<No Services>");\r
webService.add(webServiceNoServices);\r
this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
+ // this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
jMenu1.add(pasteNew);\r
jMenu1.add(pasteThis);\r
sort.add(sortIDMenuItem);\r
{\r
}\r
\r
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- }\r
-\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
{\r
}\r
{\r
}\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ protected void seqLimit_actionPerformed(ActionEvent e)\r
{\r
}\r
\r
+ public void seqDBRef_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+\r
public void createEPS(java.io.File f)\r
{\r
}\r
{\r
}\r
\r
- protected void preferences_actionPerformed(ActionEvent e)\r
+\r
+\r
+ protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ {\r
+ }\r
+\r
+ protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
{\r
}\r
\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+\r
+ public void vamsasStore_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
+ public void vamsasLoad_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+ public void showTranslation_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+ public void tabSelected()\r
+ {\r
+\r
+ }\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
\r
- protected void ClustalRealign_actionPerformed(ActionEvent e)\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
{\r
+\r
}\r
}\r
JMenuItem saveState = new JMenuItem();\r
JMenuItem loadState = new JMenuItem();\r
JMenu jMenu1 = new JMenu();\r
+ JMenuItem vamsasLoad = new JMenuItem();\r
+ JMenuItem inputSequence = new JMenuItem();\r
\r
- /**\r
+ /**\r
* Creates a new GDesktop object.\r
*/\r
public GDesktop()\r
});\r
jMenu1.setMnemonic('I');\r
jMenu1.setText("Input Alignment");\r
- DesktopMenubar.add(FileMenu);\r
+ vamsasLoad.setText("Vamsas");\r
+ vamsasLoad.setVisible(false);\r
+ vamsasLoad.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ vamsasLoad_actionPerformed(e);\r
+ }\r
+ });\r
+ inputSequence.setText("Fetch Sequence...");\r
+ inputSequence.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ inputSequence_actionPerformed(e);\r
+ }\r
+ });\r
+ DesktopMenubar.add(FileMenu);\r
DesktopMenubar.add(toolsMenu);\r
DesktopMenubar.add(HelpMenu);\r
DesktopMenubar.add(windowMenu);\r
FileMenu.addSeparator();\r
FileMenu.add(jMenu1);\r
- FileMenu.addSeparator();\r
+ FileMenu.add(inputSequence);\r
+ FileMenu.addSeparator();\r
FileMenu.add(saveState);\r
FileMenu.add(loadState);\r
FileMenu.addSeparator();\r
jMenu1.add(inputLocalFileMenuItem);\r
jMenu1.add(inputURLMenuItem);\r
jMenu1.add(inputTextboxMenuItem);\r
- }\r
+ jMenu1.add(vamsasLoad);\r
+ }\r
\r
/**\r
* DOCUMENT ME!\r
public void loadJalviewAlign_actionPerformed(ActionEvent e)\r
{\r
}\r
+\r
+ public void vamsasLoad_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
+\r
+ public void inputSequence_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
}\r
BorderLayout borderLayout1 = new BorderLayout();\r
protected JCheckBox quality = new JCheckBox();\r
JPanel visualTab = new JPanel();\r
- protected JCheckBox fullID = new JCheckBox();\r
- protected JCheckBox fullScreen = new JCheckBox();\r
+ protected JCheckBox fullScreen = new JCheckBox();\r
protected JCheckBox conservation = new JCheckBox();\r
protected JCheckBox identity = new JCheckBox();\r
protected JCheckBox annotations = new JCheckBox();\r
protected JCheckBox useProxy = new JCheckBox();\r
JPanel jPanel1 = new JPanel();\r
TitledBorder titledBorder1 = new TitledBorder("Proxy Server");\r
+ TitledBorder titledBorder2 = new TitledBorder("File Output");\r
GridBagLayout gridBagLayout2 = new GridBagLayout();\r
GridBagLayout gridBagLayout1 = new GridBagLayout();\r
GridBagLayout gridBagLayout3 = new GridBagLayout();\r
JPanel exportTab = new JPanel();\r
JLabel epsLabel = new JLabel();\r
protected JComboBox epsRendering = new JComboBox();\r
+ JLabel jLabel1 = new JLabel();\r
+ protected JCheckBox blcjv = new JCheckBox();\r
+ protected JCheckBox pileupjv = new JCheckBox();\r
+ protected JCheckBox clustaljv = new JCheckBox();\r
+ protected JCheckBox msfjv = new JCheckBox();\r
+ protected JCheckBox fastajv = new JCheckBox();\r
+ protected JCheckBox pfamjv = new JCheckBox();\r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+ protected JCheckBox pirjv = new JCheckBox();\r
+ JPanel jPanel11 = new JPanel();\r
+ Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);\r
+ protected JCheckBox seqLimit = new JCheckBox();\r
+ GridLayout gridLayout3 = new GridLayout();\r
/**\r
* Creates a new GPreferences object.\r
*/\r
}\r
});\r
quality.setEnabled(false);\r
- quality.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ quality.setFont(verdana11);\r
quality.setHorizontalAlignment(SwingConstants.RIGHT);\r
quality.setHorizontalTextPosition(SwingConstants.LEFT);\r
quality.setSelected(true);\r
quality.setText("Quality");\r
visualTab.setBorder(new TitledBorder("Open new alignment"));\r
visualTab.setLayout(null);\r
- fullID.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fullID.setHorizontalAlignment(SwingConstants.RIGHT);\r
- fullID.setHorizontalTextPosition(SwingConstants.LEFT);\r
- fullID.setMargin(new Insets(4, 2, 2, 0));\r
- fullID.setText("Full Sequence ID");\r
- fullScreen.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fullScreen.setFont(verdana11);\r
fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);\r
fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);\r
fullScreen.setMargin(new Insets(2, 2, 2, 0));\r
fullScreen.setText("Maximise Window");\r
conservation.setEnabled(false);\r
- conservation.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ conservation.setFont(verdana11);\r
conservation.setHorizontalAlignment(SwingConstants.RIGHT);\r
conservation.setHorizontalTextPosition(SwingConstants.LEFT);\r
conservation.setSelected(true);\r
conservation.setText("Conservation");\r
identity.setEnabled(false);\r
- identity.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ identity.setFont(verdana11);\r
identity.setHorizontalAlignment(SwingConstants.RIGHT);\r
identity.setHorizontalTextPosition(SwingConstants.LEFT);\r
identity.setSelected(true);\r
identity.setText("Consensus");\r
- annotations.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ annotations.setFont(verdana11);\r
annotations.setHorizontalAlignment(SwingConstants.RIGHT);\r
annotations.setHorizontalTextPosition(SwingConstants.LEFT);\r
annotations.setMargin(new Insets(2, 4, 2, 0));\r
annotations_actionPerformed(e);\r
}\r
});\r
- gapLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ gapLabel.setFont(verdana11);\r
gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
gapLabel.setText("Gap Symbol ");\r
- colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- colour.setBounds(new Rectangle(148, 171, 154, 21));\r
- colourLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ colour.setFont(verdana11);\r
+ colour.setBounds(new Rectangle(170, 170, 155, 21));\r
+ colourLabel.setFont(verdana11);\r
colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
colourLabel.setText("Colour ");\r
- fontLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontLabel.setFont(verdana11);\r
fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
fontLabel.setText("Font ");\r
- fontSizeCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontSizeCB.setFont(verdana11);\r
fontSizeCB.setBounds(new Rectangle(317, 111, 49, 21));\r
- fontStyleCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ fontStyleCB.setFont(verdana11);\r
fontStyleCB.setBounds(new Rectangle(365, 111, 70, 21));\r
- fontNameCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- fontNameCB.setBounds(new Rectangle(148, 111, 169, 21));\r
- gapSymbolCB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- gapSymbolCB.setBounds(new Rectangle(148, 141, 67, 21));\r
+ fontNameCB.setFont(verdana11);\r
+ fontNameCB.setBounds(new Rectangle(170, 111, 147, 21));\r
+ gapSymbolCB.setFont(verdana11);\r
+ gapSymbolCB.setBounds(new Rectangle(170, 141, 69, 21));\r
startupCheckbox.setText("Open file");\r
- startupCheckbox.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ startupCheckbox.setFont(verdana11);\r
startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);\r
startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);\r
startupCheckbox.setSelected(true);\r
- startupFileTextfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- startupFileTextfield.setBounds(new Rectangle(148, 232, 302, 20));\r
+ startupFileTextfield.setFont(verdana11);\r
+ startupFileTextfield.setBounds(new Rectangle(170, 232, 271, 20));\r
startupFileTextfield.addMouseListener(new MouseAdapter()\r
{\r
public void mouseClicked(MouseEvent e)\r
connectTab.setLayout(gridBagLayout3);\r
serverLabel.setText("Address");\r
serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
- serverLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- proxyServerTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- proxyPortTB.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- portLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ serverLabel.setFont(verdana11);\r
+ proxyServerTB.setFont(verdana11);\r
+ proxyPortTB.setFont(verdana11);\r
+ portLabel.setFont(verdana11);\r
portLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
portLabel.setText("Port");\r
browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11));\r
browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);\r
browserLabel.setText("Default Browser (Unix)");\r
- defaultBrowser.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ defaultBrowser.setFont(verdana11);\r
defaultBrowser.setText("");\r
newLink.setText("New");\r
newLink.addActionListener(new java.awt.event.ActionListener() {\r
linkNameList.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
linkPanel2.setLayout(borderLayout3);\r
- linkURLList.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ linkURLList.setFont(verdana11);\r
linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
\r
defaultBrowser.addMouseListener(new MouseAdapter()\r
}\r
}\r
});\r
- useProxy.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ useProxy.setFont(verdana11);\r
useProxy.setHorizontalAlignment(SwingConstants.RIGHT);\r
useProxy.setHorizontalTextPosition(SwingConstants.LEADING);\r
useProxy.setText("Use a proxy server");\r
});\r
jPanel1.setBorder(titledBorder1);\r
jPanel1.setLayout(gridBagLayout1);\r
- sortby.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- sortby.setBounds(new Rectangle(148, 200, 302, 21));\r
- sortLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ sortby.setFont(verdana11);\r
+ sortby.setBounds(new Rectangle(170, 200, 155, 21));\r
+ sortLabel.setFont(verdana11);\r
sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
sortLabel.setText("Sort by ");\r
- jPanel2.setBounds(new Rectangle(7, 17, 138, 242));\r
+ jPanel2.setBounds(new Rectangle(7, 17, 158, 242));\r
jPanel2.setLayout(gridLayout2);\r
gridLayout2.setRows(8);\r
- jPanel3.setBounds(new Rectangle(147, 46, 274, 26));\r
+ jPanel3.setBounds(new Rectangle(168, 47, 274, 26));\r
exportTab.setLayout(null);\r
- epsLabel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ epsLabel.setFont(verdana11);\r
epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);\r
epsLabel.setText("EPS Rendering Style");\r
- epsLabel.setBounds(new Rectangle(3, 47, 134, 21));\r
- epsRendering.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- epsRendering.setBounds(new Rectangle(145, 47, 286, 21));\r
+ epsLabel.setBounds(new Rectangle(9, 31, 140, 24));\r
+ epsRendering.setFont(verdana11);\r
+ epsRendering.setBounds(new Rectangle(154, 34, 187, 21));\r
+ jLabel1.setFont(verdana11);\r
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);\r
+ jLabel1.setText("Append /start-end (/15-380)");\r
+ jLabel1.setFont(verdana11);\r
+ fastajv.setFont(verdana11);\r
+ fastajv.setHorizontalAlignment(SwingConstants.LEFT);\r
+ clustaljv.setText("Clustal ");\r
+ blcjv.setText("BLC ");\r
+ fastajv.setText("Fasta ");\r
+ msfjv.setText("MSF ");\r
+ pfamjv.setText("PFAM ");\r
+ pileupjv.setText("Pileup ");\r
+ msfjv.setFont(verdana11);\r
+ msfjv.setHorizontalAlignment(SwingConstants.LEFT);\r
+ pirjv.setText("PIR ");\r
+ jPanel11.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ jPanel11.setBorder(titledBorder2);\r
+ jPanel11.setBounds(new Rectangle(30, 72, 196, 182));\r
+ jPanel11.setLayout(gridLayout3);\r
+ blcjv.setFont(verdana11);\r
+ blcjv.setHorizontalAlignment(SwingConstants.LEFT);\r
+ clustaljv.setFont(verdana11);\r
+ clustaljv.setHorizontalAlignment(SwingConstants.LEFT);\r
+ pfamjv.setFont(verdana11);\r
+ pfamjv.setHorizontalAlignment(SwingConstants.LEFT);\r
+ pileupjv.setFont(verdana11);\r
+ pileupjv.setHorizontalAlignment(SwingConstants.LEFT);\r
+ pirjv.setFont(verdana11);\r
+ pirjv.setHorizontalAlignment(SwingConstants.LEFT);\r
+ seqLimit.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);\r
+ seqLimit.setHorizontalTextPosition(SwingConstants.LEADING);\r
+ seqLimit.setText("Full Sequence Id");\r
+ gridLayout3.setRows(8);\r
jPanel2.add(fullScreen);\r
jPanel2.add(annotations);\r
- jPanel2.add(fullID);\r
+ jPanel2.add(seqLimit);\r
jPanel2.add(fontLabel);\r
jPanel2.add(gapLabel);\r
jPanel2.add(colourLabel);\r
jPanel2.add(sortLabel);\r
jPanel2.add(startupCheckbox);\r
+ visualTab.add(gapSymbolCB);\r
+ visualTab.add(colour);\r
visualTab.add(jPanel3);\r
jPanel3.add(conservation);\r
- jPanel3.add(quality);\r
jPanel3.add(identity);\r
+ jPanel3.add(quality);\r
visualTab.add(sortby);\r
- visualTab.add(colour);\r
visualTab.add(startupFileTextfield);\r
visualTab.add(fontNameCB);\r
visualTab.add(fontSizeCB);\r
visualTab.add(fontStyleCB);\r
- visualTab.add(gapSymbolCB);\r
visualTab.add(jPanel2);\r
-\r
linkPanel.add(editLinkButtons, BorderLayout.EAST);\r
editLinkButtons.add(newLink, null);\r
editLinkButtons.add(editLink, null);\r
, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,\r
new Insets(15, 0, 0, 15), 307, 1));\r
\r
- exportTab.add(epsLabel);\r
- exportTab.add(epsRendering);\r
\r
jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
, GridBagConstraints.WEST,\r
gapSymbolCB.setRenderer(dlcr);\r
\r
tabbedPane.add(visualTab, "Visual");\r
- tabbedPane.add(connectTab, "Connections");\r
- tabbedPane.add(exportTab, "Export");\r
+ tabbedPane.add(connectTab,"Connections");\r
+ tabbedPane.add(exportTab, "Output");\r
+ jPanel11.add(jLabel1);\r
+ jPanel11.add(blcjv);\r
+ jPanel11.add(clustaljv);\r
+ jPanel11.add(fastajv);\r
+ jPanel11.add(msfjv);\r
+ jPanel11.add(pfamjv);\r
+ jPanel11.add(pileupjv);\r
+ jPanel11.add(pirjv);\r
+ exportTab.add(epsLabel);\r
+ exportTab.add(epsRendering);\r
+ exportTab.add(jPanel11);\r
}\r
\r
/**\r
JMenuItem epsTree = new JMenuItem();\r
JMenu saveAsMenu = new JMenu();\r
JMenuItem textbox = new JMenuItem();\r
-\r
public GTreePanel()\r
{\r
try\r
public void textbox_actionPerformed(ActionEvent e)\r
{\r
}\r
+\r
+ public void fullid_actionPerformed(ActionEvent e)\r
+ {\r
+\r
+ }\r
}\r
propHash.put("polar", polar);\r
}\r
\r
- public static Hashtable chainColours = new Hashtable();\r
-\r
- static\r
- {\r
- chainColours.put("A", Color.red);\r
- chainColours.put("B", Color.orange);\r
- chainColours.put("C", Color.yellow);\r
- chainColours.put("D", Color.green);\r
- chainColours.put("E", Color.cyan);\r
- chainColours.put("F", Color.blue);\r
- chainColours.put("G", Color.magenta);\r
- chainColours.put("H", Color.pink);\r
- }\r
-\r
private ResidueProperties()\r
{\r
}\r
String key = (String) e.nextElement();\r
Vector tmp = (Vector) codonHash.get(key);\r
\r
- if (tmp.contains(codon))\r
+ if (tmp.contains(codon.toUpperCase()))\r
{\r
return key;\r
}\r
\r
return null;\r
}\r
-\r
- public static Hashtable getChainColours()\r
- {\r
- return chainColours;\r
- }\r
}\r
*/\r
public class Comparison\r
{\r
- /** DOCUMENT ME!! */\r
- public static String GapChars = " .-";\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ii DOCUMENT ME!\r
- * @param jj DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static float compare(SequenceI ii, SequenceI jj)\r
+ /** DOCUMENT ME!! */\r
+ public static String GapChars = " .-";\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param ii DOCUMENT ME!\r
+ * @param jj DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static float compare(SequenceI ii, SequenceI jj)\r
+ {\r
+ return Comparison.compare(ii, jj, 0, ii.getLength() - 1);\r
+ }\r
+\r
+ /**\r
+ * this was supposed to be an ungapped pid calculation\r
+ * @param ii SequenceI\r
+ * @param jj SequenceI\r
+ * @param start int\r
+ * @param end int\r
+ * @return float\r
+ */\r
+ public static float compare(SequenceI ii, SequenceI jj, int start, int end)\r
+ {\r
+ String si = ii.getSequence();\r
+ String sj = jj.getSequence();\r
+\r
+ int ilen = si.length() - 1;\r
+ int jlen = sj.length() - 1;\r
+\r
+ while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))\r
{\r
- return Comparison.compare(ii, jj, 0, ii.getLength() - 1);\r
+ ilen--;\r
}\r
\r
- /**\r
- * this was supposed to be an ungapped pid calculation\r
- * @param ii SequenceI\r
- * @param jj SequenceI\r
- * @param start int\r
- * @param end int\r
- * @return float\r
- */\r
- public static float compare(SequenceI ii, SequenceI jj, int start, int end)\r
+ while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))\r
{\r
- String si = ii.getSequence();\r
- String sj = jj.getSequence();\r
+ jlen--;\r
+ }\r
\r
- int ilen = si.length() - 1;\r
- int jlen = sj.length() - 1;\r
+ int count = 0;\r
+ int match = 0;\r
+ float pid = -1;\r
\r
- while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))\r
- {\r
- ilen--;\r
- }\r
-\r
- while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))\r
+ if (ilen > jlen)\r
+ {\r
+ for (int j = 0; j < jlen; j++)\r
+ {\r
+ if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
+ j, start + j + 1)))\r
{\r
- jlen--;\r
+ match++;\r
}\r
\r
- int count = 0;\r
- int match = 0;\r
- float pid = -1;\r
+ count++;\r
+ }\r
\r
- if (ilen > jlen)\r
- {\r
- for (int j = 0; j < jlen; j++)\r
- {\r
- if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
- j, start + j + 1)))\r
- {\r
- match++;\r
- }\r
-\r
- count++;\r
- }\r
-\r
- pid = (float) match / (float) ilen * 100;\r
- }\r
- else\r
+ pid = (float) match / (float) ilen * 100;\r
+ }\r
+ else\r
+ {\r
+ for (int j = 0; j < jlen; j++)\r
+ {\r
+ if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
+ j, start + j + 1)))\r
{\r
- for (int j = 0; j < jlen; j++)\r
- {\r
- if (si.substring(start + j, start + j + 1).equals(sj.substring(start +\r
- j, start + j + 1)))\r
- {\r
- match++;\r
- }\r
-\r
- count++;\r
- }\r
-\r
- pid = (float) match / (float) jlen * 100;\r
+ match++;\r
}\r
\r
- return pid;\r
+ count++;\r
+ }\r
+\r
+ pid = (float) match / (float) jlen * 100;\r
}\r
\r
- /**\r
- * this is a gapped PID calculation\r
- *\r
- * @param s1 SequenceI\r
- * @param s2 SequenceI\r
- * @return float\r
- */\r
- public static float PID(SequenceI s1, SequenceI s2)\r
+ return pid;\r
+ }\r
+\r
+ /**\r
+ * this is a gapped PID calculation\r
+ *\r
+ * @param s1 SequenceI\r
+ * @param s2 SequenceI\r
+ * @return float\r
+ */\r
+ public static float PID(SequenceI s1, SequenceI s2)\r
+ {\r
+ int len;\r
+\r
+ if (s1.getSequence().length() > s2.getSequence().length())\r
{\r
- int len;\r
+ len = s1.getSequence().length();\r
+ }\r
+ else\r
+ {\r
+ len = s2.getSequence().length();\r
+ }\r
\r
- if (s1.getSequence().length() > s2.getSequence().length())\r
- {\r
- len = s1.getSequence().length();\r
- }\r
- else\r
+ int bad = 0;\r
+\r
+ for (int i = 0; i < len; i++)\r
+ {\r
+ char chr1;\r
+ char chr2;\r
+\r
+ if (i < s1.getSequence().length())\r
+ {\r
+ chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
+ }\r
+ else\r
+ {\r
+ chr1 = '.';\r
+ }\r
+\r
+ if (i < s2.getSequence().length())\r
+ {\r
+ chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
+ }\r
+ else\r
+ {\r
+ chr2 = '.';\r
+ }\r
+\r
+ if (! (jalview.util.Comparison.isGap(chr1)) &&\r
+ ! (jalview.util.Comparison.isGap(chr2)))\r
+ {\r
+ if (chr1 != chr2)\r
{\r
- len = s2.getSequence().length();\r
+ bad++;\r
}\r
+ }\r
+ }\r
\r
- int bad = 0;\r
+ return ( (float) 100 * (len - bad)) / len;\r
+ }\r
\r
- for (int i = 0; i < len; i++)\r
- {\r
- char chr1;\r
- char chr2;\r
-\r
- if (i < s1.getSequence().length())\r
- {\r
- chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr1 = '.';\r
- }\r
-\r
- if (i < s2.getSequence().length())\r
- {\r
- chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr2 = '.';\r
- }\r
-\r
- if (!(jalview.util.Comparison.isGap(chr1)) &&\r
- !(jalview.util.Comparison.isGap(chr2)))\r
- {\r
- if (chr1 != chr2)\r
- {\r
- bad++;\r
- }\r
- }\r
- }\r
+ // Another pid with region specification\r
+ public static float PID(SequenceI s1, SequenceI s2, int start, int end)\r
+ {\r
+ int len;\r
\r
- return ((float) 100 * (len - bad)) / len;\r
+ if (s1.getSequence().length() > s2.getSequence().length())\r
+ {\r
+ len = s1.getSequence().length();\r
+ }\r
+ else\r
+ {\r
+ len = s2.getSequence().length();\r
}\r
\r
- // Another pid with region specification\r
- public static float PID(SequenceI s1, SequenceI s2, int start, int end)\r
+ if (end < len)\r
{\r
- int len;\r
+ len = end;\r
+ }\r
\r
- if (s1.getSequence().length() > s2.getSequence().length())\r
- {\r
- len = s1.getSequence().length();\r
- }\r
- else\r
- {\r
- len = s2.getSequence().length();\r
- }\r
+ if (len < start)\r
+ {\r
+ start = len - 1; // we just use a single residue for the difference\r
+ }\r
\r
- if (end < len)\r
- {\r
- len = end;\r
- }\r
+ int bad = 0;\r
\r
- if (len < start)\r
+ for (int i = start; i < len; i++)\r
+ {\r
+ char chr1;\r
+ char chr2;\r
+\r
+ if (i < s1.getSequence().length())\r
+ {\r
+ chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
+ }\r
+ else\r
+ {\r
+ chr1 = '.';\r
+ }\r
+\r
+ if (i < s2.getSequence().length())\r
+ {\r
+ chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
+ }\r
+ else\r
+ {\r
+ chr2 = '.';\r
+ }\r
+\r
+ if (! (jalview.util.Comparison.isGap(chr1)) &&\r
+ ! (jalview.util.Comparison.isGap(chr2)))\r
+ {\r
+ if (chr1 != chr2)\r
{\r
- start = len - 1; // we just use a single residue for the difference\r
+ bad++;\r
}\r
+ }\r
+ }\r
\r
- int bad = 0;\r
-\r
- for (int i = start; i < len; i++)\r
+ return ( (float) 100 * (len - bad)) / len;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static boolean isGap(char c)\r
+ {\r
+ return (c == '-' || c == '.' || c == ' ') ? true : false;\r
+ }\r
+\r
+ public static boolean isNucleotide(SequenceI [] seqs)\r
+ {\r
+ int i = 0, iSize = seqs.length, j, jSize;\r
+ float nt = 0, aa = 0;\r
+ char c;\r
+ while (i < iSize)\r
+ {\r
+ jSize = seqs[i].getLength();\r
+ for (j = 0; j < jSize; j++)\r
+ {\r
+ c = seqs[i].getCharAt(j);\r
+ if ('a' <= c && c <= 'z')\r
+ c -= ('a' - 'A');\r
+\r
+ if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')\r
+ nt++;\r
+ else if (!jalview.util.Comparison.isGap( seqs[i].getCharAt(j)))\r
{\r
- char chr1;\r
- char chr2;\r
-\r
- if (i < s1.getSequence().length())\r
- {\r
- chr1 = Character.toUpperCase(s1.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr1 = '.';\r
- }\r
-\r
- if (i < s2.getSequence().length())\r
- {\r
- chr2 = Character.toUpperCase(s2.getSequence().charAt(i));\r
- }\r
- else\r
- {\r
- chr2 = '.';\r
- }\r
-\r
- if (!(jalview.util.Comparison.isGap(chr1)) &&\r
- !(jalview.util.Comparison.isGap(chr2)))\r
- {\r
- if (chr1 != chr2)\r
- {\r
- bad++;\r
- }\r
- }\r
+ aa++;\r
}\r
-\r
- return ((float) 100 * (len - bad)) / len;\r
+ }\r
+ i++;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param c DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static boolean isGap(char c)\r
- {\r
- return ( c=='-' || c=='.' || c==' ' ) ? true : false;\r
- }\r
+ if ( (nt / (nt + aa)) > 0.85f)\r
+ return true;\r
+ else\r
+ return false;\r
+\r
+ }\r
}\r
--- /dev/null
+package jalview.util;\r
+\r
+import java.awt.event.ActionEvent;\r
+import java.awt.RenderingHints;\r
+import javax.imageio.ImageIO;\r
+import org.jibble.epsgraphics.EpsGraphics2D;\r
+import jalview.gui.EPSOptions;\r
+import java.awt.Graphics2D;\r
+import java.io.*;\r
+import java.awt.image.BufferedImage;\r
+import java.awt.Graphics;\r
+import jalview.io.*;\r
+import java.awt.*;\r
+\r
+\r
+public class ImageMaker\r
+{\r
+ public static final int EPS = 0;\r
+ public static final int PNG = 1;\r
+ int type = -1;\r
+\r
+ EpsGraphics2D pg;\r
+ Graphics graphics;\r
+ FileOutputStream out;\r
+ BufferedImage bi;\r
+\r
+ public ImageMaker(Component parent, int type, String title,\r
+ int width, int height, File file, String EPStitle)\r
+ {\r
+ this.type = type;\r
+\r
+ if (file == null)\r
+ {\r
+ JalviewFileChooser chooser;\r
+ chooser = type == EPS ? getEPSChooser() : getPNGChooser();\r
+\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle(title);\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(parent);\r
+\r
+ if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ file = chooser.getSelectedFile();\r
+ }\r
+ }\r
+\r
+ try\r
+ {\r
+ out = new FileOutputStream(file);\r
+\r
+ if (type == EPS)\r
+ setupEPS(width, height, EPStitle);\r
+ else\r
+ setupPNG(width, height);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Error creating " + (type == EPS ? "EPS" : "PNG") +\r
+ " file.");\r
+ }\r
+ }\r
+\r
+ public Graphics getGraphics()\r
+ {\r
+ return graphics;\r
+ }\r
+\r
+\r
+ void setupPNG(int width, int height)\r
+ {\r
+ bi = new BufferedImage(width, height,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ graphics = bi.getGraphics();\r
+ Graphics2D ig2 = (Graphics2D) graphics;\r
+ ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+ }\r
+\r
+ public void writeImage()\r
+ {\r
+ try{\r
+ switch(type)\r
+ {\r
+ case EPS:\r
+ pg.flush();\r
+ pg.close();\r
+ break;\r
+ case PNG:\r
+ ImageIO.write(bi, "png", out);\r
+ out.close();\r
+ break;\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ void setupEPS(int width, int height, String title)\r
+ {\r
+ boolean accurateText = true;\r
+\r
+ String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
+ "Prompt each time");\r
+\r
+ // If we need to prompt, and if the GUI is visible then\r
+ // Prompt for EPS rendering style\r
+ if (renderStyle.equalsIgnoreCase("Prompt each time")\r
+ && !\r
+ (System.getProperty("java.awt.headless") != null\r
+ && System.getProperty("java.awt.headless").equals("true")))\r
+ {\r
+ EPSOptions eps = new EPSOptions();\r
+ renderStyle = eps.getValue();\r
+\r
+ if (renderStyle == null || eps.cancelled)\r
+ return;\r
+ }\r
+\r
+ if (renderStyle.equalsIgnoreCase("text"))\r
+ {\r
+ accurateText = false;\r
+ }\r
+\r
+ try {\r
+ pg = new EpsGraphics2D(title, out, 0, 0, width,\r
+ height);\r
+ Graphics2D ig2 = (Graphics2D) pg;\r
+ ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+\r
+ pg.setAccurateTextMode(accurateText);\r
+\r
+ graphics = pg;\r
+ }\r
+ catch (Exception ex) { }\r
+ }\r
+\r
+\r
+ JalviewFileChooser getPNGChooser()\r
+ {\r
+ return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"png"},\r
+ new String[]\r
+ {"Portable network graphics"},\r
+ "Portable network graphics");\r
+ }\r
+\r
+ JalviewFileChooser getEPSChooser()\r
+ {\r
+ return new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"eps"},\r
+ new String[]\r
+ {"Encapsulated Postscript"},\r
+ "Encapsulated Postscript");\r
+ }\r
+}\r
msf[0].getSequence()));\r
\r
this.msa = new vamsas.objects.simple.Msfalignment();\r
- msa.setMsf(jalview.io.PileUpfile.print(msf));\r
+ jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();\r
+ msa.setMsf(pileup.print(msf));\r
}\r
\r
public void run()\r
*/\r
\r
public MsaWSClient(ext.vamsas.ServiceHandle sh, String altitle, SequenceI[] msa,\r
- boolean submitGaps, boolean preserveOrder)\r
+ boolean submitGaps, boolean preserveOrder, Alignment seqdataset)\r
{\r
\r
if (!sh.getAbstractName().equals("MsaWS"))\r
\r
return;\r
}\r
- startMsaWSClient(altitle, msa, submitGaps, preserveOrder);\r
+ startMsaWSClient(altitle, msa, submitGaps, preserveOrder, seqdataset);\r
\r
}\r
\r
\r
private void startMsaWSClient(String altitle, SequenceI[] msa,\r
- boolean submitGaps, boolean preserveOrder)\r
+ boolean submitGaps, boolean preserveOrder, Alignment seqdataset)\r
{\r
if (!locateWebService())\r
{\r
\r
MsaWSThread musclethread = new MsaWSThread(WebServiceName +\r
" alignment of " + altitle, msa,\r
- submitGaps, preserveOrder);\r
+ submitGaps, preserveOrder, seqdataset);\r
wsInfo.setthisService(musclethread);\r
musclethread.start();\r
}\r
vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.\r
SequenceSet();\r
Hashtable SeqNames = null;\r
- boolean submitGaps = false; // and always store and recover sequence order\r
+ boolean submitGaps = false; // pass sequences including gaps to alignment service\r
boolean preserveOrder = true; // and always store and recover sequence order\r
String jobId;\r
String alTitle; // name which will be used to form new alignment window.\r
int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
boolean jobComplete = false;\r
\r
+ Alignment dataset; // dataset to which the new alignment will be associated.\r
+\r
MsaWSThread(String title, SequenceI[] msa, boolean subgaps,\r
- boolean presorder)\r
+ boolean presorder, Alignment seqset)\r
{\r
alTitle = title;\r
submitGaps = subgaps;\r
preserveOrder = presorder;\r
-\r
+ dataset = seqset;\r
OutputHeader = wsInfo.getProgressText();\r
SeqNames = new Hashtable();\r
\r
jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);\r
\r
Alignment al = new Alignment(seqs);\r
-\r
+ if (dataset!=null) {\r
+ al.setDataset(dataset);\r
+ }\r
// TODO: JBPNote Should also rename the query sequence sometime...\r
AlignFrame af = new AlignFrame(al);\r
af.addSortByOrderMenuItem(ServiceName + " Ordering",\r
git://source.jalview.org / jalview.git / commitdiff