X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=4b858e144d0b3d9e3bd64a806b95671880ec72ef;hb=8a2a0cda7067530f8481c2aec203e18d555f2dfd;hp=2a2fc70d870f905f42fdcc47161a36bb314866d8;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 2a2fc70..4b858e1 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -20,6 +20,45 @@ */ package jalview.appletgui; +import java.awt.BorderLayout; +import java.awt.Canvas; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +import java.awt.FlowLayout; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.Label; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.Panel; +import java.awt.Rectangle; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusEvent; +import java.awt.event.FocusListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyEvent; +import java.awt.event.KeyListener; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.io.IOException; +import java.io.UnsupportedEncodingException; +import java.net.URL; +import java.net.URLEncoder; +import java.util.Arrays; +import java.util.Deque; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Vector; + +import org.jmol.viewer.Viewer; + import jalview.analysis.AlignmentSorter; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.analysis.TreeBuilder; @@ -81,45 +120,6 @@ import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; -import java.awt.BorderLayout; -import java.awt.Canvas; -import java.awt.CheckboxMenuItem; -import java.awt.Color; -import java.awt.FlowLayout; -import java.awt.Font; -import java.awt.FontMetrics; -import java.awt.Frame; -import java.awt.Graphics; -import java.awt.Label; -import java.awt.Menu; -import java.awt.MenuBar; -import java.awt.MenuItem; -import java.awt.Panel; -import java.awt.Rectangle; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.FocusEvent; -import java.awt.event.FocusListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.awt.event.KeyEvent; -import java.awt.event.KeyListener; -import java.awt.event.WindowAdapter; -import java.awt.event.WindowEvent; -import java.io.IOException; -import java.io.UnsupportedEncodingException; -import java.net.URL; -import java.net.URLEncoder; -import java.util.Arrays; -import java.util.Deque; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.StringTokenizer; -import java.util.Vector; - -import org.jmol.viewer.Viewer; - public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener, AlignViewControllerGuiI { @@ -1577,7 +1577,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, /* * When we finally deprecate 1.1 compatibility, we can start to use * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch - * (UnsupportedEncodingException ex) { System.err.println("WARNING - + * (UnsupportedEncodingException ex) { jalview.bin.Console.errPrintln("WARNING - * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url); * ex.printStackTrace(); } */ @@ -1586,7 +1586,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, url = viewport.applet.getCodeBase() + url; } catch (UnsupportedEncodingException ex) { - System.err.println( + jalview.bin.Console.errPrintln( "WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR " + url); ex.printStackTrace(); @@ -2975,7 +2975,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); if (viewport.applet.debug) { - System.err.println("Sorting " + alorder.getOrder().size() + jalview.bin.Console.errPrintln("Sorting " + alorder.getOrder().size() + " in alignment '" + getTitle() + "'"); } AlignmentSorter.sortBy(viewport.getAlignment(), alorder); @@ -3061,7 +3061,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { if (viewport.applet == null) { - System.out.println("Not running as applet - no browser available."); + jalview.bin.Console.outPrintln("Not running as applet - no browser available."); } else { @@ -3977,12 +3977,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, viewer = (Viewer) jmolviewer; } catch (ClassCastException ex) { - System.err.println( + jalview.bin.Console.errPrintln( "Unsupported viewer object :" + jmolviewer.getClass()); } if (viewer == null) { - System.err.println("Can't use this object as a structure viewer:" + jalview.bin.Console.errPrintln("Can't use this object as a structure viewer:" + jmolviewer.getClass()); return null; } @@ -4127,7 +4127,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, chains = (String[]) sqch[1]; if (seqs == null || seqs.length == 0) { - System.err.println( + jalview.bin.Console.errPrintln( "JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to."); } if (protocol == null) @@ -4142,7 +4142,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (protocol == null) { - System.err.println("Couldn't work out protocol to open structure: " + jalview.bin.Console.errPrintln("Couldn't work out protocol to open structure: " + pdb.getId()); return; } @@ -4154,7 +4154,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null) { - System.err.println("Failed to map " + pdb.getFile() + " (" + jalview.bin.Console.errPrintln("Failed to map " + pdb.getFile() + " (" + protocol + ") to any sequences"); } return; @@ -4176,7 +4176,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } if (ajm != null) { - System.err.println( + jalview.bin.Console.errPrintln( "Incremental adding and aligning structure to existing Jmol view not yet implemented."); // try and add the pdb structure // ajm.addS @@ -4201,7 +4201,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, SequenceI[][] seqs, String[][] chains, String[] protocols) { // TODO Auto-generated method stub - System.err.println("Aligned Structure View: Not yet implemented."); + jalview.bin.Console.errPrintln("Aligned Structure View: Not yet implemented."); } /** @@ -4258,9 +4258,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (!file.isValid()) { // TODO: raise dialog for gui - System.err.println("Problems parsing T-Coffee scores: " + jalview.bin.Console.errPrintln("Problems parsing T-Coffee scores: " + file.getWarningMessage()); - System.err.println("Origin was:\n" + source); + jalview.bin.Console.errPrintln("Origin was:\n" + source); return false; } @@ -4273,7 +4273,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, || aln.getWidth() != file.getWidth())) { // TODO: raise a dialog box here rather than bomb out. - System.err.println( + jalview.bin.Console.errPrintln( "The scores matrix does not match the alignment dimensions"); } @@ -4289,10 +4289,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else { - System.err.println("Problems resolving T-Coffee scores:"); + jalview.bin.Console.errPrintln("Problems resolving T-Coffee scores:"); if (file.getWarningMessage() != null) { - System.err.println(file.getWarningMessage()); + jalview.bin.Console.errPrintln(file.getWarningMessage()); } } return false;