From 87fc98c92b4d1083db30212139b1137b508a0c86 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 6 Dec 2005 11:42:19 +0000 Subject: [PATCH] After merge --- src/jalview/jbappletgui/GAlignFrame.java | 831 --------------------- src/jalview/jbappletgui/GAlignmentPanel.java | 100 --- src/jalview/jbappletgui/GCutAndPasteTransfer.java | 78 -- src/jalview/jbappletgui/GFinder.java | 111 --- src/jalview/jbappletgui/GFontChooser.java | 133 ---- src/jalview/jbappletgui/GPCAPanel.java | 133 ---- src/jalview/jbappletgui/GPairwiseAlignPanel.java | 59 -- src/jalview/jbappletgui/GSliderPanel.java | 115 --- src/jalview/jbappletgui/GTreePanel.java | 121 --- src/jalview/jbappletgui/GUserDefinedColours.java | 191 ----- 10 files changed, 1872 deletions(-) delete mode 100755 src/jalview/jbappletgui/GAlignFrame.java delete mode 100755 src/jalview/jbappletgui/GAlignmentPanel.java delete mode 100755 src/jalview/jbappletgui/GCutAndPasteTransfer.java delete mode 100755 src/jalview/jbappletgui/GFinder.java delete mode 100755 src/jalview/jbappletgui/GFontChooser.java delete mode 100755 src/jalview/jbappletgui/GPCAPanel.java delete mode 100755 src/jalview/jbappletgui/GPairwiseAlignPanel.java delete mode 100755 src/jalview/jbappletgui/GSliderPanel.java delete mode 100755 src/jalview/jbappletgui/GTreePanel.java delete mode 100755 src/jalview/jbappletgui/GUserDefinedColours.java diff --git a/src/jalview/jbappletgui/GAlignFrame.java b/src/jalview/jbappletgui/GAlignFrame.java deleted file mode 100755 index 7775b65..0000000 --- a/src/jalview/jbappletgui/GAlignFrame.java +++ /dev/null @@ -1,831 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbappletgui; - -import java.awt.*; -import java.awt.event.*; - - -public class GAlignFrame extends Frame { - protected MenuBar alignFrameMenuBar = new MenuBar(); - protected Menu fileMenu = new Menu(); - protected MenuItem closeMenuItem = new MenuItem(); - protected Menu editMenu = new Menu(); - protected Menu viewMenu = new Menu(); - protected Menu colourMenu = new Menu(); - protected Menu calculateMenu = new Menu(); - protected MenuItem selectAllSequenceMenuItem = new MenuItem(); - protected MenuItem deselectAllSequenceMenuItem = new MenuItem(); - protected MenuItem invertSequenceMenuItem = new MenuItem(); - protected MenuItem remove2LeftMenuItem = new MenuItem(); - protected MenuItem remove2RightMenuItem = new MenuItem(); - protected MenuItem removeGappedColumnMenuItem = new MenuItem(); - protected MenuItem removeAllGapsMenuItem = new MenuItem(); - protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); - protected MenuItem sortPairwiseMenuItem = new MenuItem(); - protected MenuItem sortIDMenuItem = new MenuItem(); - protected MenuItem sortGroupMenuItem = new MenuItem(); - protected MenuItem removeRedundancyMenuItem = new MenuItem(); - protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); - protected MenuItem PCAMenuItem = new MenuItem(); - protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); - protected MenuItem neighbourTreeMenuItem = new MenuItem(); - BorderLayout borderLayout1 = new BorderLayout(); - public Label statusBar = new Label(); - protected Menu outputTextboxMenu = new Menu(); - protected MenuItem clustalColour = new MenuItem(); - protected MenuItem zappoColour = new MenuItem(); - protected MenuItem taylorColour = new MenuItem(); - protected MenuItem hydrophobicityColour = new MenuItem(); - protected MenuItem helixColour = new MenuItem(); - protected MenuItem strandColour = new MenuItem(); - protected MenuItem turnColour = new MenuItem(); - protected MenuItem buriedColour = new MenuItem(); - protected MenuItem userDefinedColour = new MenuItem(); - protected MenuItem PIDColour = new MenuItem(); - protected MenuItem BLOSUM62Colour = new MenuItem(); - MenuItem njTreeBlosumMenuItem = new MenuItem(); - MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); - protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); - MenuItem overviewMenuItem = new MenuItem(); - protected MenuItem undoMenuItem = new MenuItem(); - protected MenuItem redoMenuItem = new MenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - MenuItem noColourmenuItem = new MenuItem(); - protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); - MenuItem findMenuItem = new MenuItem(); - Menu searchMenu = new Menu(); - protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); - protected MenuItem nucleotideColour = new MenuItem(); - MenuItem deleteGroups = new MenuItem(); - MenuItem delete = new MenuItem(); - MenuItem copy = new MenuItem(); - MenuItem cut = new MenuItem(); - Menu Menu1 = new Menu(); - MenuItem pasteNew = new MenuItem(); - MenuItem pasteThis = new MenuItem(); - protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); - protected MenuItem font = new MenuItem(); - protected CheckboxMenuItem fullSeqId = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); - MenuItem modifyPID = new MenuItem(); - MenuItem modifyConservation = new MenuItem(); - protected Menu sortByTreeMenu = new Menu(); - Menu sort = new Menu(); - Menu calculate = new Menu(); - MenuItem inputText = new MenuItem(); - Menu helpMenu = new Menu(); - MenuItem documentation = new MenuItem(); - MenuItem about = new MenuItem(); - - public GAlignFrame() { - try { - jbInit(); - setMenuBar(alignFrameMenuBar); - - MenuItem item; - - // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++) { - item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt( - i)); - item.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - saveAs_actionPerformed(e); - } - }); - - item = new MenuItem((String) jalview.io.FormatAdapter.formats.elementAt( - i)); - item.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - outputText_actionPerformed(e); - } - }); - - outputTextboxMenu.add(item); - } - } catch (Exception e) { - e.printStackTrace(); - } - } - - private void jbInit() throws Exception { - fileMenu.setLabel("File"); - closeMenuItem.setLabel("Close"); - closeMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - closeMenuItem_actionPerformed(e); - } - }); - editMenu.setLabel("Edit"); - viewMenu.setLabel("View"); - colourMenu.setLabel("Colour"); - calculateMenu.setLabel("Calculate"); - selectAllSequenceMenuItem.setLabel("Select all"); - selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - selectAllSequenceMenuItem_actionPerformed(e); - } - }); - deselectAllSequenceMenuItem.setLabel("Deselect All"); - deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - deselectAllSequenceMenuItem_actionPerformed(e); - } - }); - invertSequenceMenuItem.setLabel("Invert Selection"); - invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - invertSequenceMenuItem_actionPerformed(e); - } - }); - remove2LeftMenuItem.setLabel("Remove Left"); - remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - remove2LeftMenuItem_actionPerformed(e); - } - }); - remove2RightMenuItem.setLabel("Remove Right"); - remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - remove2RightMenuItem_actionPerformed(e); - } - }); - removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); - removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - removeGappedColumnMenuItem_actionPerformed(e); - } - }); - removeAllGapsMenuItem.setLabel("Remove All Gaps"); - removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - removeAllGapsMenuItem_actionPerformed(e); - } - }); - viewBoxesMenuItem.setLabel("Boxes"); - viewBoxesMenuItem.setState(true); - viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - viewBoxesMenuItem_actionPerformed(null); - } - }); - viewTextMenuItem.setLabel("Text"); - viewTextMenuItem.setState(true); - viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - viewTextMenuItem_actionPerformed(null); - } - }); - sortPairwiseMenuItem.setLabel("by Pairwise Identity"); - sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - sortPairwiseMenuItem_actionPerformed(e); - } - }); - sortIDMenuItem.setLabel("by ID"); - sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - sortIDMenuItem_actionPerformed(e); - } - }); - sortGroupMenuItem.setLabel("by Group"); - sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - sortGroupMenuItem_actionPerformed(e); - } - }); - removeRedundancyMenuItem.setLabel("Remove Redundancy..."); - removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - removeRedundancyMenuItem_actionPerformed(e); - } - }); - pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - pairwiseAlignmentMenuItem_actionPerformed(e); - } - }); - PCAMenuItem.setLabel("Principal Component Analysis"); - PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - PCAMenuItem_actionPerformed(e); - } - }); - averageDistanceTreeMenuItem.setLabel( - "Average Distance Using % Identity"); - averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - averageDistanceTreeMenuItem_actionPerformed(e); - } - }); - neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); - neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - neighbourTreeMenuItem_actionPerformed(e); - } - }); - alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setBackground(Color.white); - statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setText("Status bar"); - outputTextboxMenu.setLabel("Output to Textbox"); - clustalColour.setLabel("Clustalx"); - - clustalColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - clustalColour_actionPerformed(e); - } - }); - zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - zappoColour_actionPerformed(e); - } - }); - taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - taylorColour_actionPerformed(e); - } - }); - hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - hydrophobicityColour_actionPerformed(e); - } - }); - helixColour.setLabel("Helix Propensity"); - helixColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - helixColour_actionPerformed(e); - } - }); - strandColour.setLabel("Strand Propensity"); - strandColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - strandColour_actionPerformed(e); - } - }); - turnColour.setLabel("Turn Propensity"); - turnColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - turnColour_actionPerformed(e); - } - }); - buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - buriedColour_actionPerformed(e); - } - }); - userDefinedColour.setLabel("User Defined..."); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - userDefinedColour_actionPerformed(e); - } - }); - PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - PIDColour_actionPerformed(e); - } - }); - BLOSUM62Colour.setLabel("BLOSUM62 Score"); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - BLOSUM62Colour_actionPerformed(e); - } - }); - avDistanceTreeBlosumMenuItem.setLabel( - "Average Distance Using BLOSUM62"); - avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - avTreeBlosumMenuItem_actionPerformed(e); - } - }); - njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); - njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - njTreeBlosumMenuItem_actionPerformed(e); - } - }); - annotationPanelMenuItem.setActionCommand(""); - annotationPanelMenuItem.setState(true); - annotationPanelMenuItem.setLabel("Show Annotations"); - annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - annotationPanelMenuItem_actionPerformed(null); - } - }); - colourTextMenuItem.setLabel("Colour Text"); - colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - colourTextMenuItem_actionPerformed(null); - } - }); - overviewMenuItem.setLabel("Overview Window"); - overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - overviewMenuItem_actionPerformed(e); - } - }); - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); - undoMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - undoMenuItem_actionPerformed(e); - } - }); - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); - redoMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - redoMenuItem_actionPerformed(e); - } - }); - conservationMenuItem.setLabel("by Conservation"); - conservationMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - conservationMenuItem_actionPerformed(null); - } - }); - noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - noColourmenuItem_actionPerformed(e); - } - }); - wrapMenuItem.setLabel("Wrap"); - wrapMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - wrapMenuItem_actionPerformed(null); - } - }); - renderGapsMenuItem.setLabel("Show Gaps"); - renderGapsMenuItem.setState(true); - renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - renderGapsMenuItem_actionPerformed(null); - } - }); - findMenuItem.setLabel("Find..."); - findMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - findMenuItem_actionPerformed(e); - } - }); - searchMenu.setLabel("Search"); - - abovePIDThreshold.setLabel("Above Identity Threshold"); - abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - abovePIDThreshold_actionPerformed(null); - } - }); - nucleotideColour.setLabel("Nucleotide"); - nucleotideColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - nucleotideColour_actionPerformed(e); - } - }); - deleteGroups.setLabel("Undefine Groups"); - deleteGroups.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - deleteGroups_actionPerformed(e); - } - }); - copy.setLabel("Copy"); - copy.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); - } - }); - cut.setLabel("Cut"); - cut.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); - } - }); - delete.setLabel("Delete"); - delete.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - delete_actionPerformed(e); - } - }); - Menu1.setLabel("Paste"); - pasteNew.setLabel("To New Alignment"); - pasteNew.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - pasteNew_actionPerformed(e); - } - }); - pasteThis.setLabel("Add To This Alignment"); - pasteThis.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - pasteThis_actionPerformed(e); - } - }); - applyToAllGroups.setLabel("Apply Colour To All Groups"); - applyToAllGroups.setState(true); - applyToAllGroups.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - applyToAllGroups_actionPerformed(null); - } - }); - font.setLabel("Font..."); - font.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - font_actionPerformed(e); - } - }); - fullSeqId.setLabel("Show Full Sequence ID"); - fullSeqId.setState(true); - fullSeqId.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - fullSeqId_actionPerformed(null); - } - }); - scaleAbove.setLabel("Scale Above"); - scaleAbove.setState(true); - scaleAbove.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - scaleAbove_actionPerformed(null); - } - }); - scaleLeft.setEnabled(false); - scaleLeft.setState(true); - scaleLeft.setLabel("Scale Left"); - scaleLeft.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - scaleLeft_actionPerformed(null); - } - }); - scaleRight.setEnabled(false); - scaleRight.setState(true); - scaleRight.setLabel("Scale Right"); - scaleRight.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - scaleRight_actionPerformed(null); - } - }); - modifyPID.setLabel("Modify Identity Threshold..."); - modifyPID.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - modifyPID_actionPerformed(e); - } - }); - modifyConservation.setLabel("Modify Conservation Threshold..."); - modifyConservation.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - modifyConservation_actionPerformed(e); - } - }); - sortByTreeMenu.setLabel("By Tree Order"); - sort.setLabel("Sort"); - calculate.setLabel("Calculate Tree"); - inputText.setLabel("Input from textbox"); - inputText.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - inputText_actionPerformed(e); - } - }); - - helpMenu.setLabel("Help"); - documentation.setLabel("Documentation"); - documentation.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - documentation_actionPerformed(e); - } - }); - - about.setLabel("About..."); - about.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - about_actionPerformed(e); - } - }); - - alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(searchMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(colourMenu); - alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(helpMenu); - fileMenu.add(inputText); - fileMenu.add(outputTextboxMenu); - fileMenu.addSeparator(); - fileMenu.add(closeMenuItem); - editMenu.add(undoMenuItem); - editMenu.add(redoMenuItem); - editMenu.add(cut); - editMenu.add(copy); - editMenu.add(Menu1); - editMenu.add(delete); - editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.add(deleteGroups); - editMenu.addSeparator(); - editMenu.add(remove2LeftMenuItem); - editMenu.add(remove2RightMenuItem); - editMenu.add(removeGappedColumnMenuItem); - editMenu.add(removeAllGapsMenuItem); - editMenu.add(removeRedundancyMenuItem); - searchMenu.add(findMenuItem); - viewMenu.add(font); - viewMenu.addSeparator(); - viewMenu.add(wrapMenuItem); - viewMenu.add(scaleAbove); - viewMenu.add(scaleLeft); - viewMenu.add(scaleRight); - viewMenu.addSeparator(); - viewMenu.add(fullSeqId); - viewMenu.add(viewBoxesMenuItem); - viewMenu.add(viewTextMenuItem); - viewMenu.add(colourTextMenuItem); - viewMenu.add(renderGapsMenuItem); - viewMenu.add(annotationPanelMenuItem); - viewMenu.addSeparator(); - viewMenu.add(overviewMenuItem); - colourMenu.add(applyToAllGroups); - colourMenu.addSeparator(); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideColour); - colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(modifyConservation); - colourMenu.add(abovePIDThreshold); - colourMenu.add(modifyPID); - calculateMenu.add(sort); - calculateMenu.add(calculate); - calculateMenu.addSeparator(); - calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); - this.add(statusBar, BorderLayout.SOUTH); - Menu1.add(pasteNew); - Menu1.add(pasteThis); - sort.add(sortIDMenuItem); - sort.add(sortByTreeMenu); - sort.add(sortGroupMenuItem); - sort.add(sortPairwiseMenuItem); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.add(njTreeBlosumMenuItem); - helpMenu.add(documentation); - helpMenu.add(about); - } - - protected void saveAs_actionPerformed(ActionEvent e) { - } - - protected void outputText_actionPerformed(ActionEvent e) { - } - - protected void htmlMenuItem_actionPerformed(ActionEvent e) { - } - - protected void closeMenuItem_actionPerformed(ActionEvent e) { - } - - protected void redoMenuItem_actionPerformed(ActionEvent e) { - } - - protected void undoMenuItem_actionPerformed(ActionEvent e) { - } - - protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - } - - protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { - } - - protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) { - } - - protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) { - } - - protected void remove2RightMenuItem_actionPerformed(ActionEvent e) { - } - - protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { - } - - protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { - } - - protected void wrapMenuItem_actionPerformed(ActionEvent e) { - } - - protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) { - } - - protected void viewTextMenuItem_actionPerformed(ActionEvent e) { - } - - protected void colourTextMenuItem_actionPerformed(ActionEvent e) { - } - - protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) { - } - - protected void overviewMenuItem_actionPerformed(ActionEvent e) { - } - - protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { - } - - protected void sortIDMenuItem_actionPerformed(ActionEvent e) { - } - - protected void sortGroupMenuItem_actionPerformed(ActionEvent e) { - } - - protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { - } - - protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { - } - - protected void PCAMenuItem_actionPerformed(ActionEvent e) { - } - - protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { - } - - protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { - } - - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - } - - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { - } - - protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) { - } - - protected void clustalColour_actionPerformed(ActionEvent e) { - } - - protected void zappoColour_actionPerformed(ActionEvent e) { - } - - protected void taylorColour_actionPerformed(ActionEvent e) { - } - - protected void hydrophobicityColour_actionPerformed(ActionEvent e) { - } - - protected void helixColour_actionPerformed(ActionEvent e) { - } - - protected void strandColour_actionPerformed(ActionEvent e) { - } - - protected void turnColour_actionPerformed(ActionEvent e) { - } - - protected void buriedColour_actionPerformed(ActionEvent e) { - } - - protected void userDefinedColour_actionPerformed(ActionEvent e) { - } - - protected void PIDColour_actionPerformed(ActionEvent e) { - } - - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) { - } - - protected void noColourmenuItem_actionPerformed(ActionEvent e) { - } - - protected void conservationMenuItem_actionPerformed(ActionEvent e) { - } - - protected void printMenuItem_actionPerformed(ActionEvent e) { - } - - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { - } - - protected void findMenuItem_actionPerformed(ActionEvent e) { - } - - protected void abovePIDThreshold_actionPerformed(ActionEvent e) { - } - - public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) { - } - - protected void nucleotideColour_actionPerformed(ActionEvent e) { - } - - protected void deleteGroups_actionPerformed(ActionEvent e) { - } - - protected void copy_actionPerformed(ActionEvent e) { - } - - protected void cut_actionPerformed(ActionEvent e) { - } - - protected void delete_actionPerformed(ActionEvent e) { - } - - protected void pasteNew_actionPerformed(ActionEvent e) { - } - - protected void pasteThis_actionPerformed(ActionEvent e) { - } - - protected void applyToAllGroups_actionPerformed(ActionEvent e) { - } - - protected void createPNG_actionPerformed(ActionEvent e) { - } - - protected void font_actionPerformed(ActionEvent e) { - } - - protected void fullSeqId_actionPerformed(ActionEvent e) { - } - - protected void epsFile_actionPerformed(ActionEvent e) { - } - - protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { - } - - protected void jpred_actionPerformed(ActionEvent e) { - } - - protected void scaleAbove_actionPerformed(ActionEvent e) { - } - - protected void scaleLeft_actionPerformed(ActionEvent e) { - } - - protected void scaleRight_actionPerformed(ActionEvent e) { - } - - protected void modifyPID_actionPerformed(ActionEvent e) { - } - - protected void modifyConservation_actionPerformed(ActionEvent e) { - } - - protected void preferences_actionPerformed(ActionEvent e) { - } - - protected void msaAlignMenuItem_actionPerformed(ActionEvent e) { - } - - protected void inputText_actionPerformed(ActionEvent e) { - } - - protected void documentation_actionPerformed(ActionEvent e) { - } - - protected void about_actionPerformed(ActionEvent e) { - } -} diff --git a/src/jalview/jbappletgui/GAlignmentPanel.java b/src/jalview/jbappletgui/GAlignmentPanel.java deleted file mode 100755 index 683c9c1..0000000 --- a/src/jalview/jbappletgui/GAlignmentPanel.java +++ /dev/null @@ -1,100 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbappletgui; - -import java.awt.*; - - -public class GAlignmentPanel extends Panel { - protected Panel sequenceHolderPanel = new Panel(); - protected Scrollbar vscroll = new Scrollbar(); - protected Scrollbar hscroll = new Scrollbar(); - protected Panel seqPanelHolder = new Panel(); - BorderLayout borderLayout1 = new BorderLayout(); - BorderLayout borderLayout3 = new BorderLayout(); - protected Panel scalePanelHolder = new Panel(); - protected Panel idPanelHolder = new Panel(); - BorderLayout borderLayout5 = new BorderLayout(); - protected Panel idSpaceFillerPanel1 = new Panel(); - public Panel annotationSpaceFillerHolder = new Panel(); - BorderLayout borderLayout6 = new BorderLayout(); - BorderLayout borderLayout7 = new BorderLayout(); - Panel hscrollHolder = new Panel(); - BorderLayout borderLayout10 = new BorderLayout(); - protected Panel hscrollFillerPanel = new Panel(); - BorderLayout borderLayout11 = new BorderLayout(); - public Panel annotationScroller = new Panel(); - BorderLayout borderLayout4 = new BorderLayout(); - BorderLayout borderLayout2 = new BorderLayout(); - - public GAlignmentPanel() { - try { - jbInit(); - } catch (Exception e) { - e.printStackTrace(); - } - } - - private void jbInit() throws Exception { - // idPanelHolder.setPreferredSize(new Dimension(70, 10)); - this.setLayout(borderLayout7); - - // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150)); - sequenceHolderPanel.setLayout(borderLayout3); - seqPanelHolder.setLayout(borderLayout1); - scalePanelHolder.setBackground(Color.white); - - // scalePanelHolder.setPreferredSize(new Dimension(10, 30)); - scalePanelHolder.setLayout(borderLayout6); - idPanelHolder.setLayout(borderLayout5); - idSpaceFillerPanel1.setBackground(Color.white); - - // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30)); - idSpaceFillerPanel1.setLayout(borderLayout11); - annotationSpaceFillerHolder.setBackground(Color.white); - - // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80)); - annotationSpaceFillerHolder.setLayout(borderLayout4); - hscroll.setOrientation(Scrollbar.HORIZONTAL); - hscrollHolder.setLayout(borderLayout10); - hscrollFillerPanel.setBackground(Color.white); - - // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10)); - hscrollHolder.setBackground(Color.white); - - // annotationScroller.setPreferredSize(new Dimension(10, 80)); - // this.setPreferredSize(new Dimension(220, 166)); - seqPanelHolder.setBackground(Color.white); - idPanelHolder.setBackground(Color.white); - annotationScroller.setLayout(borderLayout2); - sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH); - sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER); - seqPanelHolder.add(vscroll, BorderLayout.EAST); - sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH); - - // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH); - this.add(idPanelHolder, BorderLayout.WEST); - idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH); - idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH); - this.add(hscrollHolder, BorderLayout.SOUTH); - hscrollHolder.add(hscroll, BorderLayout.CENTER); - hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST); - this.add(sequenceHolderPanel, BorderLayout.CENTER); - } -} diff --git a/src/jalview/jbappletgui/GCutAndPasteTransfer.java b/src/jalview/jbappletgui/GCutAndPasteTransfer.java deleted file mode 100755 index 907ec0a..0000000 --- a/src/jalview/jbappletgui/GCutAndPasteTransfer.java +++ /dev/null @@ -1,78 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbappletgui; - -import java.awt.*; -import java.awt.event.*; - - -public class GCutAndPasteTransfer extends Panel { - protected TextArea textarea = new TextArea(); - Button ok = new Button(); - Button cancel = new Button(); - protected Panel buttonPanel = new Panel(); - BorderLayout borderLayout1 = new BorderLayout(); - - public GCutAndPasteTransfer() { - try { - jbInit(); - } catch (Exception e) { - e.printStackTrace(); - } - } - - private void jbInit() throws Exception { - textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10)); - textarea.setText("Paste your alignment file here"); - textarea.addMouseListener(new java.awt.event.MouseAdapter() { - public void mousePressed(MouseEvent e) { - textarea_mousePressed(e); - } - }); - this.setLayout(borderLayout1); - ok.setLabel("OK"); - ok.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - ok_actionPerformed(e); - } - }); - cancel.setLabel("Cancel"); - cancel.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - cancel_actionPerformed(e); - } - }); - this.add(buttonPanel, BorderLayout.SOUTH); - buttonPanel.add(ok, null); - buttonPanel.add(cancel, null); - this.add(textarea, java.awt.BorderLayout.CENTER); - } - - void textarea_mousePressed(MouseEvent e) { - if (textarea.getText().equals("Paste your alignment file here")) { - textarea.setText(""); - } - } - - protected void ok_actionPerformed(ActionEvent e) { - } - - protected void cancel_actionPerformed(ActionEvent e) { - } -} diff --git a/src/jalview/jbappletgui/GFinder.java b/src/jalview/jbappletgui/GFinder.java deleted file mode 100755 index 434c8ea..0000000 --- a/src/jalview/jbappletgui/GFinder.java +++ /dev/null @@ -1,111 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbappletgui; - -import java.awt.*; -import java.awt.event.*; - - -public class GFinder extends Panel { - Label jLabel1 = new Label(); - protected TextField textfield = new TextField(); - protected Button findAll = new Button(); - protected Button findNext = new Button(); - Panel jPanel1 = new Panel(); - GridLayout gridLayout1 = new GridLayout(); - protected Button createNewGroup = new Button(); - - public GFinder() { - try { - jbInit(); - } catch (Exception e) { - e.printStackTrace(); - } - } - - private void jbInit() throws Exception { - jLabel1.setFont(new java.awt.Font("Verdana", 0, 12)); - jLabel1.setText("Find"); - jLabel1.setBounds(new Rectangle(3, 30, 34, 15)); - this.setLayout(null); - textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - textfield.setText(""); - textfield.setBounds(new Rectangle(40, 27, 133, 21)); - textfield.addKeyListener(new java.awt.event.KeyAdapter() { - public void keyTyped(KeyEvent e) { - textfield_keyTyped(e); - } - }); - textfield.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - textfield_actionPerformed(e); - } - }); - findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - findAll.setLabel("Find all"); - findAll.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - findAll_actionPerformed(e); - } - }); - findNext.setEnabled(false); - findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - findNext.setLabel("Find Next"); - findNext.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - findNext_actionPerformed(e); - } - }); - jPanel1.setBounds(new Rectangle(180, 5, 141, 64)); - jPanel1.setLayout(gridLayout1); - gridLayout1.setHgap(0); - gridLayout1.setRows(3); - gridLayout1.setVgap(2); - createNewGroup.setEnabled(false); - createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10)); - createNewGroup.setLabel("Create new group"); - createNewGroup.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - createNewGroup_actionPerformed(e); - } - }); - jPanel1.add(findNext, null); - jPanel1.add(findAll, null); - jPanel1.add(createNewGroup, null); - this.add(textfield, null); - this.add(jLabel1, null); - this.add(jPanel1, null); - } - - protected void findNext_actionPerformed(ActionEvent e) { - } - - protected void findAll_actionPerformed(ActionEvent e) { - } - - protected void textfield_actionPerformed(ActionEvent e) { - } - - void textfield_keyTyped(KeyEvent e) { - findNext.setEnabled(true); - } - - public void createNewGroup_actionPerformed(ActionEvent e) { - } -} diff --git a/src/jalview/jbappletgui/GFontChooser.java b/src/jalview/jbappletgui/GFontChooser.java deleted file mode 100755 index 794dbbb..0000000 --- a/src/jalview/jbappletgui/GFontChooser.java +++ /dev/null @@ -1,133 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbappletgui; - -import java.awt.*; -import java.awt.event.*; - - -public class GFontChooser extends Panel { - Label label1 = new Label(); - protected Choice fontSize = new Choice(); - protected Choice fontStyle = new Choice(); - Label label2 = new Label(); - Label label3 = new Label(); - protected Choice fontName = new Choice(); - Button ok = new Button(); - Button cancel = new Button(); - Panel panel1 = new Panel(); - Panel panel2 = new Panel(); - Panel panel3 = new Panel(); - BorderLayout borderLayout1 = new BorderLayout(); - BorderLayout borderLayout2 = new BorderLayout(); - BorderLayout borderLayout3 = new BorderLayout(); - Panel panel4 = new Panel(); - Panel panel5 = new Panel(); - BorderLayout borderLayout4 = new BorderLayout(); - - public GFontChooser() { - try { - jbInit(); - } catch (Exception e) { - e.printStackTrace(); - } - } - - private void jbInit() throws Exception { - label1.setFont(new java.awt.Font("Verdana", 0, 11)); - label1.setAlignment(Label.RIGHT); - label1.setText("Font: "); - this.setLayout(borderLayout4); - fontSize.setFont(new java.awt.Font("Verdana", 0, 11)); - fontSize.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - fontSize_actionPerformed(); - } - }); - fontStyle.setFont(new java.awt.Font("Verdana", 0, 11)); - fontStyle.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - fontStyle_actionPerformed(); - } - }); - label2.setAlignment(Label.RIGHT); - label2.setFont(new java.awt.Font("Verdana", 0, 11)); - label2.setText("Size: "); - label3.setAlignment(Label.RIGHT); - label3.setFont(new java.awt.Font("Verdana", 0, 11)); - label3.setText("Style: "); - fontName.setFont(new java.awt.Font("Verdana", 0, 11)); - fontName.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - fontName_actionPerformed(); - } - }); - ok.setFont(new java.awt.Font("Verdana", 0, 11)); - ok.setLabel("OK"); - ok.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - ok_actionPerformed(); - } - }); - cancel.setFont(new java.awt.Font("Verdana", 0, 11)); - cancel.setLabel("Cancel"); - cancel.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - cancel_actionPerformed(); - } - }); - this.setBackground(Color.white); - panel1.setLayout(borderLayout1); - panel2.setLayout(borderLayout3); - panel3.setLayout(borderLayout2); - panel5.setBackground(Color.white); - panel4.setBackground(Color.white); - panel1.setBackground(Color.white); - panel2.setBackground(Color.white); - panel3.setBackground(Color.white); - panel1.add(label1, BorderLayout.WEST); - panel1.add(fontName, BorderLayout.CENTER); - panel5.add(panel1, null); - panel5.add(panel3, null); - panel5.add(panel2, null); - panel2.add(label3, BorderLayout.WEST); - panel2.add(fontStyle, BorderLayout.CENTER); - panel3.add(label2, BorderLayout.WEST); - panel3.add(fontSize, BorderLayout.CENTER); - this.add(panel4, BorderLayout.SOUTH); - panel4.add(ok, null); - panel4.add(cancel, null); - this.add(panel5, BorderLayout.CENTER); - } - - protected void ok_actionPerformed() { - } - - protected void cancel_actionPerformed() { - } - - protected void fontName_actionPerformed() { - } - - protected void fontSize_actionPerformed() { - } - - protected void fontStyle_actionPerformed() { - } -} diff --git a/src/jalview/jbappletgui/GPCAPanel.java b/src/jalview/jbappletgui/GPCAPanel.java deleted file mode 100755 index d67d1c3..0000000 --- a/src/jalview/jbappletgui/GPCAPanel.java +++ /dev/null @@ -1,133 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbappletgui; - -import java.awt.*; -import java.awt.event.*; - - -public class GPCAPanel extends Frame { - Panel jPanel2 = new Panel(); - Label jLabel1 = new Label(); - Label jLabel2 = new Label(); - Label jLabel3 = new Label(); - protected Choice xCombobox = new Choice(); - protected Choice yCombobox = new Choice(); - protected Choice zCombobox = new Choice(); - FlowLayout flowLayout1 = new FlowLayout(); - BorderLayout borderLayout1 = new BorderLayout(); - MenuBar menuBar1 = new MenuBar(); - Menu menu1 = new Menu(); - Menu menu2 = new Menu(); - protected CheckboxMenuItem labels = new CheckboxMenuItem(); - MenuItem values = new MenuItem(); - - public GPCAPanel() { - try { - jbInit(); - } catch (Exception e) { - e.printStackTrace(); - } - - for (int i = 1; i < 8; i++) { - xCombobox.addItem("dim " + i); - yCombobox.addItem("dim " + i); - zCombobox.addItem("dim " + i); - } - } - - private void jbInit() throws Exception { - this.setLayout(borderLayout1); - jPanel2.setLayout(flowLayout1); - jLabel1.setFont(new java.awt.Font("Verdana", 0, 12)); - jLabel1.setText("x="); - jLabel2.setFont(new java.awt.Font("Verdana", 0, 12)); - jLabel2.setText("y="); - jLabel3.setFont(new java.awt.Font("Verdana", 0, 12)); - jLabel3.setText("z="); - jPanel2.setBackground(Color.white); - zCombobox.setFont(new java.awt.Font("Verdana", 0, 12)); - zCombobox.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - zCombobox_actionPerformed(null); - } - }); - yCombobox.setFont(new java.awt.Font("Verdana", 0, 12)); - yCombobox.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - yCombobox_actionPerformed(null); - } - }); - xCombobox.setFont(new java.awt.Font("Verdana", 0, 12)); - xCombobox.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - xCombobox_actionPerformed(null); - } - }); - this.setMenuBar(menuBar1); - menu1.setLabel("File"); - menu2.setLabel("View"); - labels.setLabel("Labels"); - labels.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) - { - labels_itemStateChanged(itemEvent); - } - }); - values.setLabel("Output Values..."); - values.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent actionEvent) - { - values_actionPerformed(actionEvent); - } - }); - this.add(jPanel2, BorderLayout.SOUTH); - jPanel2.add(jLabel1, null); - jPanel2.add(xCombobox, null); - jPanel2.add(jLabel2, null); - jPanel2.add(yCombobox, null); - jPanel2.add(jLabel3, null); - jPanel2.add(zCombobox, null); - menuBar1.add(menu1); - menuBar1.add(menu2); - menu2.add(labels); - menu1.add(values); - } - - protected void xCombobox_actionPerformed(ActionEvent e) { - } - - protected void yCombobox_actionPerformed(ActionEvent e) { - } - - protected void zCombobox_actionPerformed(ActionEvent e) { - } - - public void values_actionPerformed(ActionEvent actionEvent) - { - - } - - public void labels_itemStateChanged(ItemEvent itemEvent) - { - - } -} diff --git a/src/jalview/jbappletgui/GPairwiseAlignPanel.java b/src/jalview/jbappletgui/GPairwiseAlignPanel.java deleted file mode 100755 index 10bd01e..0000000 --- a/src/jalview/jbappletgui/GPairwiseAlignPanel.java +++ /dev/null @@ -1,59 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbappletgui; - -import java.awt.*; -import java.awt.event.*; - - -public class GPairwiseAlignPanel extends Panel { - protected ScrollPane scrollPane = new ScrollPane(); - protected TextArea textarea = new TextArea(); - protected Button viewInEditorButton = new Button(); - Panel jPanel1 = new Panel(); - BorderLayout borderLayout1 = new BorderLayout(); - - public GPairwiseAlignPanel() { - try { - jbInit(); - } catch (Exception e) { - e.printStackTrace(); - } - } - - private void jbInit() throws Exception { - this.setLayout(borderLayout1); - textarea.setFont(new java.awt.Font("Monospaced", 0, 12)); - textarea.setText(""); - viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12)); - viewInEditorButton.setLabel("View in alignment editor"); - viewInEditorButton.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - viewInEditorButton_actionPerformed(e); - } - }); - this.add(scrollPane, BorderLayout.CENTER); - scrollPane.add(textarea); - this.add(jPanel1, BorderLayout.SOUTH); - jPanel1.add(viewInEditorButton, null); - } - - protected void viewInEditorButton_actionPerformed(ActionEvent e) { - } -} diff --git a/src/jalview/jbappletgui/GSliderPanel.java b/src/jalview/jbappletgui/GSliderPanel.java deleted file mode 100755 index 5e33300..0000000 --- a/src/jalview/jbappletgui/GSliderPanel.java +++ /dev/null @@ -1,115 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbappletgui; - -import java.awt.*; -import java.awt.event.*; - - -public class GSliderPanel extends Panel { - // this is used for conservation colours, PID colours and redundancy threshold - protected Scrollbar slider = new Scrollbar(); - protected TextField valueField = new TextField(); - protected Label label = new Label(); - Panel jPanel1 = new Panel(); - Panel jPanel2 = new Panel(); - protected Button applyButton = new Button(); - protected Button undoButton = new Button(); - FlowLayout flowLayout1 = new FlowLayout(); - protected Checkbox allGroupsCheck = new Checkbox(); - BorderLayout borderLayout1 = new BorderLayout(); - BorderLayout borderLayout2 = new BorderLayout(); - FlowLayout flowLayout2 = new FlowLayout(); - - public GSliderPanel() { - try { - jbInit(); - } catch (Exception e) { - e.printStackTrace(); - } - } - - private void jbInit() throws Exception { - this.setLayout(borderLayout2); - - // slider.setMajorTickSpacing(10); - // slider.setMinorTickSpacing(1); - // slider.setPaintTicks(true); - slider.setBackground(Color.white); - slider.setFont(new java.awt.Font("Verdana", 0, 11)); - slider.setOrientation(0); - valueField.setFont(new java.awt.Font("Verdana", 0, 11)); - valueField.setText(" "); - valueField.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - valueField_actionPerformed(e); - } - }); - label.setFont(new java.awt.Font("Verdana", 0, 11)); - label.setText("set this label text"); - jPanel1.setLayout(borderLayout1); - jPanel2.setLayout(flowLayout1); - applyButton.setFont(new java.awt.Font("Verdana", 0, 11)); - applyButton.setLabel("Apply"); - applyButton.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - applyButton_actionPerformed(e); - } - }); - undoButton.setEnabled(false); - undoButton.setFont(new java.awt.Font("Verdana", 0, 11)); - undoButton.setLabel("Undo"); - undoButton.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - undoButton_actionPerformed(e); - } - }); - allGroupsCheck.setEnabled(false); - allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11)); - allGroupsCheck.setLabel("Apply threshold to all groups"); - allGroupsCheck.setName("Apply to all Groups"); - allGroupsCheck.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - allGroupsCheck_actionPerformed(); - } - }); - this.setBackground(Color.white); - this.setForeground(Color.black); - jPanel2.add(label, null); - jPanel2.add(applyButton, null); - jPanel2.add(undoButton, null); - jPanel2.add(allGroupsCheck); - jPanel1.add(valueField, java.awt.BorderLayout.EAST); - jPanel1.add(slider, java.awt.BorderLayout.CENTER); - this.add(jPanel1, java.awt.BorderLayout.SOUTH); - this.add(jPanel2, java.awt.BorderLayout.CENTER); - } - - protected void valueField_actionPerformed(ActionEvent e) { - } - - protected void applyButton_actionPerformed(ActionEvent e) { - } - - protected void undoButton_actionPerformed(ActionEvent e) { - } - - protected void allGroupsCheck_actionPerformed() { - } -} diff --git a/src/jalview/jbappletgui/GTreePanel.java b/src/jalview/jbappletgui/GTreePanel.java deleted file mode 100755 index bfe6b2b..0000000 --- a/src/jalview/jbappletgui/GTreePanel.java +++ /dev/null @@ -1,121 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbappletgui; - -import java.awt.*; -import java.awt.event.*; - - -public class GTreePanel extends Frame { - BorderLayout borderLayout1 = new BorderLayout(); - protected ScrollPane scrollPane = new ScrollPane(); - MenuBar jMenuBar1 = new MenuBar(); - Menu jMenu2 = new Menu(); - protected MenuItem fontSize = new MenuItem(); - protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem(); - protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem(); - protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem(); - protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem(); - Menu fileMenu = new Menu(); - MenuItem newickOutput = new MenuItem(); - - public GTreePanel() { - try { - jbInit(); - this.setMenuBar(jMenuBar1); - } catch (Exception e) { - e.printStackTrace(); - } - } - - private void jbInit() throws Exception { - setLayout(borderLayout1); - this.setBackground(Color.white); - this.setFont(new java.awt.Font("Verdana", 0, 12)); - jMenu2.setLabel("View"); - fontSize.setLabel("Font..."); - fontSize.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - fontSize_actionPerformed(e); - } - }); - bootstrapMenu.setLabel("Show Bootstrap Values"); - bootstrapMenu.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - bootstrapMenu_actionPerformed(null); - } - }); - distanceMenu.setLabel("Show Distances"); - distanceMenu.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - distanceMenu_actionPerformed(null); - } - }); - placeholdersMenu.setLabel("Mark Unassociated Leaves"); - placeholdersMenu.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - placeholdersMenu_actionPerformed(null); - } - }); - fitToWindow.setState(true); - fitToWindow.setLabel("Fit To Window"); - fitToWindow.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - fitToWindow_actionPerformed(null); - } - }); - fileMenu.setLabel("File"); - newickOutput.setLabel("Newick Format"); - newickOutput.addActionListener(new ActionListener() { - public void actionPerformed(ActionEvent actionEvent) { - newickOutput_actionPerformed(actionEvent); - } - }); - add(scrollPane, BorderLayout.CENTER); - jMenuBar1.add(fileMenu); - jMenuBar1.add(jMenu2); - jMenu2.add(fitToWindow); - jMenu2.add(fontSize); - jMenu2.add(distanceMenu); - jMenu2.add(bootstrapMenu); - jMenu2.add(placeholdersMenu); - fileMenu.add(newickOutput); - } - - protected void printMenu_actionPerformed(ActionEvent e) { - } - - protected void fontSize_actionPerformed(ActionEvent e) { - } - - protected void distanceMenu_actionPerformed(ActionEvent e) { - } - - protected void bootstrapMenu_actionPerformed(ActionEvent e) { - } - - protected void placeholdersMenu_actionPerformed(ActionEvent e) { - } - - protected void fitToWindow_actionPerformed(ActionEvent e) { - } - - public void newickOutput_actionPerformed(ActionEvent actionEvent) { - } -} diff --git a/src/jalview/jbappletgui/GUserDefinedColours.java b/src/jalview/jbappletgui/GUserDefinedColours.java deleted file mode 100755 index b26dd9a..0000000 --- a/src/jalview/jbappletgui/GUserDefinedColours.java +++ /dev/null @@ -1,191 +0,0 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ -package jalview.jbappletgui; - -import java.awt.*; -import java.awt.event.*; - - -public class GUserDefinedColours extends Panel { - protected Panel buttonPanel = new Panel(); - protected GridLayout gridLayout = new GridLayout(); - Panel jPanel2 = new Panel(); - protected Button okButton = new Button(); - protected Button applyButton = new Button(); - protected Button cancelButton = new Button(); - protected Scrollbar rScroller = new Scrollbar(); - Label label1 = new Label(); - protected TextField rText = new TextField(); - Label label4 = new Label(); - protected Scrollbar gScroller = new Scrollbar(); - protected TextField gText = new TextField(); - Label label5 = new Label(); - protected Scrollbar bScroller = new Scrollbar(); - protected TextField bText = new TextField(); - protected Panel target = new Panel(); - - public GUserDefinedColours() { - try { - jbInit(); - } catch (Exception e) { - e.printStackTrace(); - } - } - - private void jbInit() throws Exception { - this.setLayout(null); - buttonPanel.setLayout(gridLayout); - gridLayout.setColumns(6); - gridLayout.setRows(4); - okButton.setFont(new java.awt.Font("Verdana", 0, 11)); - okButton.setLabel("OK"); - okButton.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - okButton_actionPerformed(e); - } - }); - applyButton.setFont(new java.awt.Font("Verdana", 0, 11)); - applyButton.setLabel("Apply"); - applyButton.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - applyButton_actionPerformed(e); - } - }); - cancelButton.setFont(new java.awt.Font("Verdana", 0, 11)); - cancelButton.setLabel("Cancel"); - cancelButton.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - cancelButton_actionPerformed(e); - } - }); - this.setBackground(new Color(212, 208, 223)); - jPanel2.setBounds(new Rectangle(0, 265, 400, 35)); - buttonPanel.setBounds(new Rectangle(0, 123, 400, 142)); - rScroller.setMaximum(256); - rScroller.setMinimum(0); - rScroller.setOrientation(0); - rScroller.setUnitIncrement(1); - rScroller.setVisibleAmount(1); - rScroller.setBounds(new Rectangle(36, 27, 119, 19)); - rScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() { - public void adjustmentValueChanged(AdjustmentEvent e) { - rScroller_adjustmentValueChanged(e); - } - }); - label1.setAlignment(Label.RIGHT); - label1.setText("R"); - label1.setBounds(new Rectangle(19, 30, 16, 15)); - rText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10)); - rText.setText("0 "); - rText.setBounds(new Rectangle(156, 27, 53, 19)); - rText.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - rText_actionPerformed(e); - } - }); - label4.setAlignment(Label.RIGHT); - label4.setText("G"); - label4.setBounds(new Rectangle(15, 56, 20, 15)); - gScroller.setMaximum(256); - gScroller.setMinimum(0); - gScroller.setOrientation(0); - gScroller.setUnitIncrement(1); - gScroller.setVisibleAmount(1); - gScroller.setBounds(new Rectangle(35, 52, 120, 20)); - gScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() { - public void adjustmentValueChanged(AdjustmentEvent e) { - gScroller_adjustmentValueChanged(e); - } - }); - gText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10)); - gText.setText("0 "); - gText.setBounds(new Rectangle(156, 52, 53, 20)); - gText.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - gText_actionPerformed(e); - } - }); - label5.setAlignment(Label.RIGHT); - label5.setText("B"); - label5.setBounds(new Rectangle(14, 82, 20, 15)); - bScroller.setMaximum(256); - bScroller.setMinimum(0); - bScroller.setOrientation(0); - bScroller.setUnitIncrement(1); - bScroller.setVisibleAmount(1); - bScroller.setBounds(new Rectangle(35, 78, 120, 20)); - bScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() { - public void adjustmentValueChanged(AdjustmentEvent e) { - bScroller_adjustmentValueChanged(e); - } - }); - bText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10)); - bText.setText("0 "); - bText.setBounds(new Rectangle(157, 78, 52, 20)); - bText.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - bText_actionPerformed(e); - } - }); - target.setBackground(Color.black); - target.setBounds(new Rectangle(229, 26, 134, 79)); - this.add(jPanel2, null); - jPanel2.add(okButton, null); - jPanel2.add(applyButton, null); - jPanel2.add(cancelButton, null); - this.add(buttonPanel, null); - this.add(target, null); - this.add(gScroller); - this.add(rScroller); - this.add(bScroller); - this.add(label5); - this.add(label4); - this.add(label1); - this.add(gText); - this.add(rText); - this.add(bText); - } - - protected void okButton_actionPerformed(ActionEvent e) { - } - - protected void applyButton_actionPerformed(ActionEvent e) { - } - - protected void cancelButton_actionPerformed(ActionEvent e) { - } - - protected void rScroller_adjustmentValueChanged(AdjustmentEvent e) { - } - - protected void gScroller_adjustmentValueChanged(AdjustmentEvent e) { - } - - protected void bScroller_adjustmentValueChanged(AdjustmentEvent e) { - } - - protected void rText_actionPerformed(ActionEvent e) { - } - - protected void gText_actionPerformed(ActionEvent e) { - } - - protected void bText_actionPerformed(ActionEvent e) { - } -} -- 1.7.10.2