X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=0dde2550942de057b4f08f8622e1cd9a07cdec04;hb=aa643d0f2f5f506df2771e216af1618549d32050;hp=e9c54167ff87ecbb6baec20de853e7c6224ab19b;hpb=e739c2824d4d6a93c3e0f255780259c7daf2dc21;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index e9c5416..0dde255 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -20,36 +20,36 @@ */ package jalview.gui; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.gui.StructureViewer.ViewerType; -import jalview.structures.models.AAStructureBindingModel; -import jalview.util.BrowserLauncher; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.ws.dbsources.Pdb; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; import java.awt.Rectangle; -import java.awt.event.ActionEvent; import java.io.File; import java.util.ArrayList; import java.util.List; -import java.util.Vector; -import javax.swing.JCheckBoxMenuItem; import javax.swing.JPanel; import javax.swing.JSplitPane; import javax.swing.SwingUtilities; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.StructureViewer.ViewerType; +import jalview.structure.StructureCommand; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.BrowserLauncher; +import jalview.util.ImageMaker; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.dbsources.Pdb; + public class AppJmol extends StructureViewerBase { // ms to wait for Jmol to load files @@ -154,14 +154,6 @@ public class AppJmol extends StructureViewerBase .getString("label.let_jmol_manage_structure_colours")); } - IProgressIndicator progressBar = null; - - @Override - protected IProgressIndicator getIProgressIndicator() - { - return progressBar; - } - /** * display a single PDB structure in a new Jmol view * @@ -173,7 +165,7 @@ public class AppJmol extends StructureViewerBase public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, final AlignmentPanel ap) { - progressBar = ap.alignFrame; + setProgressIndicator(ap.alignFrame); openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry }, new SequenceI[][] @@ -184,14 +176,17 @@ public class AppJmol extends StructureViewerBase PDBEntry[] pdbentrys, SequenceI[][] seqs) { - progressBar = ap.alignFrame; + setProgressIndicator(ap.alignFrame); jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); alignAddedStructures = alignAdded; - useAlignmentPanelForSuperposition(ap); + if (pdbentrys.length > 1) + { + useAlignmentPanelForSuperposition(ap); + } jmb.setColourBySequence(true); setSize(400, 400); // probably should be a configurable/dynamic default here @@ -254,30 +249,12 @@ public class AppJmol extends StructureViewerBase { command = ""; } - jmb.evalStateCommand(command); - jmb.evalStateCommand("set hoverDelay=0.1"); + jmb.executeCommand(new StructureCommand(command), false); + jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false); jmb.setFinishedInit(true); } @Override - void showSelectedChains() - { - Vector toshow = new Vector<>(); - for (int i = 0; i < chainMenu.getItemCount(); i++) - { - if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) - { - JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i); - if (item.isSelected()) - { - toshow.addElement(item.getText()); - } - } - } - jmb.centerViewer(toshow); - } - - @Override public void closeViewer(boolean closeExternalViewer) { // Jmol does not use an external viewer @@ -350,12 +327,12 @@ public class AppJmol extends StructureViewerBase cmd.append("loadingJalviewdata=true\nload APPEND "); cmd.append(filesString); cmd.append("\nloadingJalviewdata=null"); - final String command = cmd.toString(); + final StructureCommand command = new StructureCommand(cmd.toString()); lastnotify = jmb.getLoadNotifiesHandled(); try { - jmb.evalStateCommand(command); + jmb.executeCommand(command, false); } catch (OutOfMemoryError oomerror) { new OOMWarning("When trying to add structures to the Jmol viewer!", @@ -396,7 +373,7 @@ public class AppJmol extends StructureViewerBase } // refresh the sequence colours for the new structure(s) - for (AlignmentPanel ap : _colourwith) + for (AlignmentViewPanel ap : _colourwith) { jmb.updateColours(ap); } @@ -418,7 +395,7 @@ public class AppJmol extends StructureViewerBase @Override public void run() { - if (jmb.viewer.isScriptExecuting()) + if (jmb.jmolViewer.isScriptExecuting()) { SwingUtilities.invokeLater(this); try @@ -431,7 +408,7 @@ public class AppJmol extends StructureViewerBase } else { - alignStructs_withAllAlignPanels(); + alignStructsWithAllAlignPanels(); } } }); @@ -469,12 +446,9 @@ public class AppJmol extends StructureViewerBase AlignmentI pdbseq = null; pdbid = jmb.getPdbEntry(pi).getId(); long hdl = pdbid.hashCode() - System.currentTimeMillis(); - if (progressBar != null) - { - progressBar.setProgressBar(MessageManager - .formatMessage("status.fetching_pdb", new String[] - { pdbid }), hdl); - } + setProgressMessage(MessageManager + .formatMessage("status.fetching_pdb", new String[] + { pdbid }), hdl); try { pdbseq = pdbclient.getSequenceRecords(pdbid); @@ -487,12 +461,8 @@ public class AppJmol extends StructureViewerBase errormsgs.append("'").append(pdbid).append("'"); } finally { - if (progressBar != null) - { - progressBar.setProgressBar( - MessageManager.getString("label.state_completed"), - hdl); - } + setProgressMessage( + MessageManager.getString("label.state_completed"), hdl); } if (pdbseq != null) { @@ -550,53 +520,52 @@ public class AppJmol extends StructureViewerBase } @Override - public void eps_actionPerformed(ActionEvent e) + public void eps_actionPerformed() { - makePDBImage(jalview.util.ImageMaker.TYPE.EPS); + makePDBImage(ImageMaker.TYPE.EPS); } @Override - public void png_actionPerformed(ActionEvent e) + public void png_actionPerformed() { - makePDBImage(jalview.util.ImageMaker.TYPE.PNG); + makePDBImage(ImageMaker.TYPE.PNG); } - void makePDBImage(jalview.util.ImageMaker.TYPE type) + void makePDBImage(ImageMaker.TYPE type) { int width = getWidth(); int height = getHeight(); - jalview.util.ImageMaker im; + ImageMaker im; - if (type == jalview.util.ImageMaker.TYPE.PNG) + if (type == ImageMaker.TYPE.PNG) { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view", + im = new ImageMaker(this, ImageMaker.TYPE.PNG, + "Make PNG image from view", width, height, null, null, null, 0, false); } - else if (type == jalview.util.ImageMaker.TYPE.EPS) + else if (type == ImageMaker.TYPE.EPS) { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view", + im = new ImageMaker(this, ImageMaker.TYPE.EPS, + "Make EPS file from view", width, height, null, this.getTitle(), null, 0, false); } else { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", + ImageMaker.TYPE.SVG, "Make SVG file from PCA", width, height, null, this.getTitle(), null, 0, false); } if (im.getGraphics() != null) { - jmb.viewer.renderScreenImage(im.getGraphics(), width, height); + jmb.jmolViewer.renderScreenImage(im.getGraphics(), width, height); im.writeImage(); } } @Override - public void showHelp_actionPerformed(ActionEvent actionEvent) + public void showHelp_actionPerformed() { try { @@ -608,9 +577,9 @@ public class AppJmol extends StructureViewerBase } } + @Override public void showConsole(boolean showConsole) { - if (showConsole) { if (splitPane == null) @@ -676,7 +645,7 @@ public class AppJmol extends StructureViewerBase } } } - else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit()) + else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit()) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -687,7 +656,7 @@ public class AppJmol extends StructureViewerBase } else { - jmb.viewer.renderScreenImage(g, currentSize.width, + jmb.jmolViewer.renderScreenImage(g, currentSize.width, currentSize.height); } } @@ -700,12 +669,6 @@ public class AppJmol extends StructureViewerBase } @Override - public String getStateInfo() - { - return jmb == null ? null : jmb.viewer.getStateInfo(); - } - - @Override public ViewerType getViewerType() { return ViewerType.JMOL;