X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBViewer.java;h=916e920e8f8e4c8b92909c5c48bd61d96dae3ca1;hb=3eafed0b5aa42e74ac0ec9681a2b3c308b7bb495;hp=ce2083ae91449e3008b3dc763b9b3903b496fc28;hpb=fbf0a6e1eb4869dc676334a30c9e40b60a7659ac;p=jalview.git diff --git a/src/MCview/AppletPDBViewer.java b/src/MCview/AppletPDBViewer.java index ce2083a..916e920 100755 --- a/src/MCview/AppletPDBViewer.java +++ b/src/MCview/AppletPDBViewer.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 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 @@ -19,126 +19,165 @@ package MCview; import java.awt.*; - import java.awt.event.*; -import jalview.datamodel.*; + import jalview.appletgui.*; +import jalview.datamodel.*; import jalview.schemes.*; -import java.awt.event.ActionListener; -import java.awt.event.ActionEvent; - +import jalview.structure.StructureListener; +import jalview.structure.*; -public class AppletPDBViewer extends Frame implements ActionListener, ItemListener +public class AppletPDBViewer + extends Frame implements ActionListener, ItemListener { - AppletPDBCanvas pdbcanvas; - public AppletPDBViewer(String pdbtext,String type, - Sequence seq, - SeqCanvas seqcanvas) - { + AppletPDBCanvas pdbcanvas; - try - { - jbInit(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } + public AppletPDBViewer(PDBEntry pdbentry, + SequenceI[] seq, + AlignmentPanel ap, + String protocol) + { + try + { + jbInit(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } - pdbcanvas = new AppletPDBCanvas(seqcanvas, seq); + pdbcanvas = new AppletPDBCanvas(pdbentry, seq, ap, protocol); - add(pdbcanvas, BorderLayout.CENTER); - StringBuffer title = new StringBuffer(seq.getName() + ":"); + add(pdbcanvas, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this,title.toString(),400, 400); + StringBuffer title = new StringBuffer(seq[0].getName() + + ":" + + pdbcanvas.pdbentry.getFile()); - try{ - PDBfile pdbfile = new PDBfile(pdbtext, type); - pdbcanvas.setPDBFile(pdbfile); - } - catch(Exception ex){ - ex.printStackTrace(); - pdbcanvas.errorLoading = true; - pdbcanvas.repaint(); - } - } + jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400); + + } - public void actionPerformed(ActionEvent evt) - { - if(evt.getSource()==mapping) - mapping_actionPerformed(); - else if(evt.getSource()==wire) - wire_actionPerformed(); - else if(evt.getSource()==depth) - depth_actionPerformed(); - else if(evt.getSource()==zbuffer) - zbuffer_actionPerformed(); - else if(evt.getSource()==charge) - charge_actionPerformed(); - else if(evt.getSource()==chain) - chain_actionPerformed(); - else if(evt.getSource()==seqButton) - seqButton_actionPerformed(); - else if(evt.getSource()==zappo) - pdbcanvas.setColours(new ZappoColourScheme()); - else if(evt.getSource()==taylor) - pdbcanvas.setColours(new TaylorColourScheme()); - else if(evt.getSource()==hydro) - pdbcanvas.setColours(new HydrophobicColourScheme()); - else if(evt.getSource()==helix) - pdbcanvas.setColours(new HelixColourScheme()); - else if(evt.getSource()==strand) - pdbcanvas.setColours(new StrandColourScheme()); - else if(evt.getSource()==turn) - pdbcanvas.setColours(new TurnColourScheme()); - else if(evt.getSource()==buried) - pdbcanvas.setColours(new BuriedColourScheme()); - else if(evt.getSource()==user) - { - pdbcanvas.bysequence = false; - new jalview.appletgui.UserDefinedColours(pdbcanvas); - } - } - public void itemStateChanged(ItemEvent evt) - { - if (evt.getSource() == allchains) - allchains_itemStateChanged(); - else if (evt.getSource() == wire) - wire_actionPerformed(); - else if (evt.getSource() == depth) - depth_actionPerformed(); - else if (evt.getSource() == zbuffer) - zbuffer_actionPerformed(); - } + public void actionPerformed(ActionEvent evt) + { + if (evt.getSource() == mapping) + { + jalview.appletgui.CutAndPasteTransfer cap + = new jalview.appletgui.CutAndPasteTransfer(false, null); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, + 600); + cap.setText(pdbcanvas.mappingDetails.toString()); + + } + else if (evt.getSource() == charge) + { + pdbcanvas.bysequence = false; + pdbcanvas.pdb.setChargeColours(); + } + + else if (evt.getSource() == chain) + { + pdbcanvas.bysequence = false; + pdbcanvas.pdb.setChainColours(); + } + else if (evt.getSource() == seqButton) + { + pdbcanvas.bysequence = true; + pdbcanvas.colourBySequence(pdbcanvas.ap.getSequenceRenderer(), + pdbcanvas.ap.av.getShowSequenceFeatures() ? + pdbcanvas.ap.getFeatureRenderer() : null); + + } + else if (evt.getSource() == zappo) + { + pdbcanvas.setColours(new ZappoColourScheme()); + } + else if (evt.getSource() == taylor) + { + pdbcanvas.setColours(new TaylorColourScheme()); + } + else if (evt.getSource() == hydro) + { + pdbcanvas.setColours(new HydrophobicColourScheme()); + } + else if (evt.getSource() == helix) + { + pdbcanvas.setColours(new HelixColourScheme()); + } + else if (evt.getSource() == strand) + { + pdbcanvas.setColours(new StrandColourScheme()); + } + else if (evt.getSource() == turn) + { + pdbcanvas.setColours(new TurnColourScheme()); + } + else if (evt.getSource() == buried) + { + pdbcanvas.setColours(new BuriedColourScheme()); + } + else if (evt.getSource() == user) + { + pdbcanvas.bysequence = false; + new jalview.appletgui.UserDefinedColours(pdbcanvas); + } + + pdbcanvas.redrawneeded = true; + pdbcanvas.repaint(); + + } + public void itemStateChanged(ItemEvent evt) + { + if (evt.getSource() == allchains) + { + pdbcanvas.setAllchainsVisible(allchains.getState()); + } + else if (evt.getSource() == wire) + { + pdbcanvas.wire = !pdbcanvas.wire; + } + else if (evt.getSource() == depth) + { + pdbcanvas.depthcue = !pdbcanvas.depthcue; + } + else if (evt.getSource() == zbuffer) + { + pdbcanvas.zbuffer = !pdbcanvas.zbuffer; + } + pdbcanvas.redrawneeded = true; + pdbcanvas.repaint(); + } - private void jbInit() - throws Exception - { - setMenuBar(jMenuBar1); - fileMenu.setLabel("File"); - coloursMenu.setLabel("Colours"); - mapping.setLabel("View Mapping"); - mapping.addActionListener(this); - wire.setLabel("Wireframe"); - wire.addItemListener(this); - depth.setState(true); - depth.setLabel("Depthcue"); - depth.addItemListener(this); - zbuffer.setState(true); - zbuffer.setLabel("Z Buffering"); - zbuffer.addItemListener(this); - charge.setLabel("Charge & Cysteine"); - charge.addActionListener(this); - hydro.setLabel("Hydrophobicity"); - hydro.addActionListener(this); - chain.setLabel("By Chain"); - chain.addActionListener(this); - seqButton.setLabel("By Sequence"); - seqButton.addActionListener(this); + private void jbInit() + throws Exception + { + setMenuBar(jMenuBar1); + fileMenu.setLabel("File"); + coloursMenu.setLabel("Colours"); + mapping.setLabel("View Mapping"); + mapping.addActionListener(this); + wire.setLabel("Wireframe"); + wire.addItemListener(this); + depth.setState(true); + depth.setLabel("Depthcue"); + depth.addItemListener(this); + zbuffer.setState(true); + zbuffer.setLabel("Z Buffering"); + zbuffer.addItemListener(this); + charge.setLabel("Charge & Cysteine"); + charge.addActionListener(this); + hydro.setLabel("Hydrophobicity"); + hydro.addActionListener(this); + chain.setLabel("By Chain"); + chain.addActionListener(this); + seqButton.setLabel("By Sequence"); + seqButton.addActionListener(this); allchains.setLabel("All Chains Visible"); allchains.addItemListener(this); viewMenu.setLabel("View"); @@ -157,12 +196,12 @@ public class AppletPDBViewer extends Frame implements ActionListener, ItemListen user.setLabel("User Defined..."); user.addActionListener(this); jMenuBar1.add(fileMenu); - jMenuBar1.add(coloursMenu); + jMenuBar1.add(coloursMenu); jMenuBar1.add(viewMenu); - fileMenu.add(mapping);; + fileMenu.add(mapping); ; - coloursMenu.add(seqButton); - coloursMenu.add(chain); + coloursMenu.add(seqButton); + coloursMenu.add(chain); coloursMenu.add(charge); coloursMenu.add(zappo); coloursMenu.add(taylor); @@ -179,21 +218,21 @@ public class AppletPDBViewer extends Frame implements ActionListener, ItemListen allchains.setState(true); } - MenuBar jMenuBar1 = new MenuBar(); - Menu fileMenu = new Menu(); - Menu coloursMenu = new Menu(); - MenuItem mapping = new MenuItem(); - CheckboxGroup bg = new CheckboxGroup(); - CheckboxMenuItem wire = new CheckboxMenuItem(); - CheckboxMenuItem depth = new CheckboxMenuItem(); - CheckboxMenuItem zbuffer = new CheckboxMenuItem(); - - MenuItem charge = new MenuItem(); - MenuItem hydro = new MenuItem(); - MenuItem chain = new MenuItem(); - MenuItem seqButton = new MenuItem(); - - CheckboxMenuItem allchains = new CheckboxMenuItem(); + MenuBar jMenuBar1 = new MenuBar(); + Menu fileMenu = new Menu(); + Menu coloursMenu = new Menu(); + MenuItem mapping = new MenuItem(); + CheckboxGroup bg = new CheckboxGroup(); + CheckboxMenuItem wire = new CheckboxMenuItem(); + CheckboxMenuItem depth = new CheckboxMenuItem(); + CheckboxMenuItem zbuffer = new CheckboxMenuItem(); + + MenuItem charge = new MenuItem(); + MenuItem hydro = new MenuItem(); + MenuItem chain = new MenuItem(); + MenuItem seqButton = new MenuItem(); + + CheckboxMenuItem allchains = new CheckboxMenuItem(); Menu viewMenu = new Menu(); MenuItem turn = new MenuItem(); MenuItem strand = new MenuItem(); @@ -203,64 +242,9 @@ public class AppletPDBViewer extends Frame implements ActionListener, ItemListen MenuItem buried = new MenuItem(); MenuItem user = new MenuItem(); - public void charge_actionPerformed() - { - pdbcanvas.bysequence = false; - pdbcanvas.pdb.setChargeColours(); - pdbcanvas.redrawneeded=true; - pdbcanvas.repaint(); - } - - public void chain_actionPerformed() - { - pdbcanvas.bysequence = false; - pdbcanvas.pdb.setChainColours(); - pdbcanvas.redrawneeded=true; - pdbcanvas.repaint(); - } - - public void zbuffer_actionPerformed() - { - pdbcanvas.zbuffer = ! pdbcanvas.zbuffer; - pdbcanvas.redrawneeded=true; - pdbcanvas.repaint(); - } - - public void depth_actionPerformed() - { - pdbcanvas.depthcue = ! pdbcanvas.depthcue; - pdbcanvas.redrawneeded=true; - pdbcanvas.repaint(); - } - - public void wire_actionPerformed() - { - pdbcanvas.wire = ! pdbcanvas.wire; - pdbcanvas.redrawneeded=true; - pdbcanvas.repaint(); - } - - public void seqButton_actionPerformed() - { - pdbcanvas.bysequence = true; - pdbcanvas.updateSeqColours(); - pdbcanvas.repaint(); - } - - public void mapping_actionPerformed() - { - jalview.appletgui.CutAndPasteTransfer cap - = new jalview.appletgui.CutAndPasteTransfer(false, null); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500, 600); - cap.setText(pdbcanvas.mappingDetails.toString()); - } +//End StructureListener +//////////////////////////// - public void allchains_itemStateChanged() - { - pdbcanvas.setAllchainsVisible(allchains.getState()); - } }