\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.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
public final AlignViewport viewport;\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
+\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 dbref = new CheckboxMenuItem();\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
+ dbref.setLabel("ShowSequence DB Refs");\r
+ dbref.setActionCommand("");\r
+ dbref.setState(true);\r
+ dbref.addItemListener(new java.awt.event.ItemListener() {\r
+ public void itemStateChanged(ItemEvent e) {\r
+ dbref_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(dbref);\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
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
seqPanel.seqCanvas.repaint();\r
scalePanel.repaint();\r
annotationPanel.repaint();\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
public void drawComponent(Graphics g, int width)\r
{\r
- if (!jalview.bin.JalviewLite.AWT1)\r
- {\r
- MyGraphics.AntiAlias(g);\r
- }\r
-\r
FontMetrics fm = g.getFontMetrics(g.getFont());\r
g.setColor(Color.white);\r
g.fillRect(0, 0, getSize().width, getSize().height);\r
fastPaint = false;\r
}\r
\r
- if (!jalview.bin.JalviewLite.AWT1)\r
- {\r
- MyGraphics.AntiAlias(gg);\r
- }\r
-\r
-\r
if (fastPaint)\r
{\r
g.drawImage(image, 0, 0, this);\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
\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
af.statusBar.setText("Successfully pasted alignment file");\r
}\r
}\r
- Frame frame = (Frame)this.getParent();\r
- frame.setVisible(false);\r
+\r
+ setVisible(false);\r
}\r
\r
protected void cancel_actionPerformed(ActionEvent e)\r
{\r
- Frame frame = (Frame)this.getParent();\r
- frame.setVisible(false);\r
+ setVisible(false);\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().equals("Paste your alignment file here")) {\r
+ textarea.setText("");\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.setFont(av.getFont());\r
}\r
\r
- if(!jalview.bin.JalviewLite.AWT1)\r
- {\r
- MyGraphics.AntiAlias(gg);\r
- }\r
-\r
-\r
//Fill in the background\r
gg.setColor(Color.white);\r
Font italic = new Font(av.getFont().getName(), Font.ITALIC,\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
"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 (!jalview.bin.JalviewLite.AWT1)\r
- {\r
- MyGraphics.AntiAlias(g);\r
- }\r
-\r
if (points == null)\r
{\r
g.setFont(new Font("Verdana", Font.PLAIN, 18));\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
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
public void drawScale(Graphics gg, int startx, int endx, int width,\r
int height)\r
{\r
- if (!jalview.bin.JalviewLite.AWT1)\r
- {\r
- MyGraphics.AntiAlias(gg);\r
- }\r
-\r
gg.setFont(av.getFont());\r
\r
//Fill in the background\r
{\r
img = createImage(imgWidth, imgHeight);\r
gg = img.getGraphics();\r
- if(!jalview.bin.JalviewLite.AWT1)\r
- {\r
- MyGraphics.AntiAlias(gg);\r
- }\r
gg.setFont(av.getFont());\r
}\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
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
if(tree==null)\r
return;\r
\r
- if (!jalview.bin.JalviewLite.AWT1)\r
- {\r
- MyGraphics.AntiAlias(g);\r
- }\r
-\r
g.setFont(font);\r
\r
\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
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
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
+ CheckboxMenuItem fullId = new CheckboxMenuItem();\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
+ fullId.setLabel("Show Full Id");\r
+ fullId.addItemListener(new ItemListener()\r
+ {\r
+ public void itemStateChanged(ItemEvent itemEvent)\r
+ {\r
+ fullId_itemStateChanged(itemEvent);\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
+ jMenu2.add(fullId);\r
+ fullId.setState(true);\r
+ fileMenu.add(newickOutput);\r
+ }\r
+\r
+\r
+ public void fullId_itemStateChanged(ItemEvent itemEvent)\r
+ {\r
+ tree.findHeight(tree.getTopNode());\r
+\r
+ // Now have to calculate longest name based on the leaves\r
+ Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());\r
+\r
+ treeCanvas.longestName="";\r
+ for (int i = 0; i < leaves.size(); i++)\r
+ {\r
+ SequenceNode lf = (SequenceNode) leaves.elementAt(i);\r
+ Sequence seq = (Sequence) lf.element();\r
+ lf.setName(seq.getDisplayId(fullId.getState(), false));\r
+ if(lf.getName().length() > treeCanvas.longestName.length())\r
+ treeCanvas.longestName = lf.getName();\r
+ }\r
+\r
+ treeCanvas.repaint();\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
git://source.jalview.org / jalview.git / commitdiff