From: jprocter Date: Fri, 18 Jan 2013 10:50:24 +0000 (+0000) Subject: Merge branch 'JAL-1254-hotfix' into develop X-Git-Tag: Jalview_2_9~254 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=48eed205662848798c4ff2d21d3e184d135b9e83;hp=71b2ce7380030c11554a5f3a1f3d82db320f0b14;p=jalview.git Merge branch 'JAL-1254-hotfix' into develop --- diff --git a/examples/appletParameters.html b/examples/appletParameters.html index 427c8b7..3b10c14 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -80,7 +80,11 @@ function mcancelclosetime() document.onclick = mclose; // --> - + @@ -88,10 +92,10 @@ document.onclick = mclose; @@ -100,39 +104,38 @@ document.onclick = mclose; @@ -546,7 +549,7 @@ document.onclick = mclose;
  • Note parameter "PDBSeq" is no longer required.
    • -
  • Jalview 2.3 was updated to work with Jmol 11. See the versions archive if you want to download the old Jmol applet.
    • +
  • Jalview 2.3 was updated to work with Jmol 11. See the versions archive if you want to download the old Jmol applet.

    •  

    @@ -599,18 +602,5 @@ Bioinformatics 25 (9) 1189-1191 - var gaJsHost = (("https:" == document.location.protocol) ? - "https://ssl." : "http://www."); - document.write(unescape("%3Cscript src=\'" + gaJsHost + - "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E")); - - diff --git a/examples/applets.html b/examples/applets.html index e3e1d3c..c53cc7a 100755 --- a/examples/applets.html +++ b/examples/applets.html @@ -79,7 +79,11 @@ function mcancelclosetime() document.onclick = mclose; // --> - + @@ -87,10 +91,10 @@ document.onclick = mclose; @@ -99,39 +103,38 @@ document.onclick = mclose; @@ -319,4 +322,4 @@ Bioinformatics 25 (9) 1189-1191 + @@ -87,10 +91,10 @@ document.onclick = mclose; @@ -99,39 +103,38 @@ document.onclick = mclose; diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html index 86dceea..5a65953 100644 --- a/examples/embeddedWJmol.html +++ b/examples/embeddedWJmol.html @@ -19,6 +19,11 @@ Embedded JalviewLite talking to externally managed Jmol + @@ -177,10 +182,10 @@ document.onclick = mclose; @@ -189,39 +194,38 @@ document.onclick = mclose; @@ -269,18 +273,5 @@ Bioinformatics 25 (9) 1189-1191 - var gaJsHost = (("https:" == document.location.protocol) ? - "https://ssl." : "http://www."); - document.write(unescape("%3Cscript src=\'" + gaJsHost + - "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E")); - - diff --git a/examples/formComplete.html b/examples/formComplete.html index 71a904a..91b0670 100644 --- a/examples/formComplete.html +++ b/examples/formComplete.html @@ -79,7 +79,11 @@ function mcancelclosetime() document.onclick = mclose; // --> - + @@ -87,10 +91,10 @@ document.onclick = mclose; @@ -99,39 +103,38 @@ document.onclick = mclose; @@ -218,18 +221,6 @@ Bioinformatics 25 (9) 1189-1191 - var gaJsHost = (("https:" == document.location.protocol) ? - "https://ssl." : "http://www."); - document.write(unescape("%3Cscript src=\'" + gaJsHost + - "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E")); - - + - \ No newline at end of file + diff --git a/examples/jalviewLiteJs.html b/examples/jalviewLiteJs.html index 5d0af5d..0e8b78a 100644 --- a/examples/jalviewLiteJs.html +++ b/examples/jalviewLiteJs.html @@ -80,7 +80,9 @@ function mcancelclosetime() document.onclick = mclose; // --> - + @@ -88,10 +90,10 @@ document.onclick = mclose; @@ -100,39 +102,38 @@ document.onclick = mclose; @@ -422,17 +423,5 @@ Bioinformatics 25 (9) 1189-1191 - var gaJsHost = (("https:" == document.location.protocol) ? - "https://ssl." : "http://www."); - document.write(unescape("%3Cscript src=\'" + gaJsHost + - "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E")); - - + diff --git a/examples/javascriptLaunch.html b/examples/javascriptLaunch.html index 7dbf8e0..f555265 100644 --- a/examples/javascriptLaunch.html +++ b/examples/javascriptLaunch.html @@ -79,7 +79,9 @@ function mcancelclosetime() document.onclick = mclose; // --> - + @@ -87,10 +89,10 @@ document.onclick = mclose; @@ -99,39 +101,38 @@ document.onclick = mclose; @@ -267,19 +268,6 @@ Bioinformatics 25 (9) 1189-1191 - var gaJsHost = (("https:" == document.location.protocol) ? - "https://ssl." : "http://www."); - document.write(unescape("%3Cscript src=\'" + gaJsHost + - "google-analytics.com/ga.js\' type=\'text/javascript\'%3E%3C/script%3E")); - - - \ No newline at end of file + diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html index 4296146..86f4bc0 100644 --- a/examples/linkedapplets_ng.html +++ b/examples/linkedapplets_ng.html @@ -23,6 +23,11 @@ + - diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index c85de33..3d54ae1 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -762,7 +762,7 @@ public class AnnotationLabels extends Panel implements ActionListener, dragEvent.getY()); } - if ((aa == null) || (aa.length < 1)) + if (!av.wrapAlignment && ((aa == null) || (aa.length < 1))) { g.setColor(Color.black); g.drawString("Right click", 2, 8); diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 1577477..dd6f190 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -960,7 +960,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, dragEvent.getY() - scrollOffset); } - if ((aa == null) || (aa.length < 1)) + if (!av.wrapAlignment && ((aa == null) || (aa.length < 1))) { g.drawString("Right click", 2, 8); g.drawString("to add annotation", 2, 18); diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 90808de..65f65bb 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -318,7 +318,10 @@ public class AnnotationRenderer updateFromAwtRenderPanel(annotPanel, av); fm = g.getFontMetrics(); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); - + if (aa==null) + { + return false; + } int x = 0, y = 0; int column = 0; char lastSS; diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 1a21fea..8ad14e0 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -23,6 +23,7 @@ import jalview.gui.Desktop; import jalview.gui.JvSwingUtils; import jalview.ws.WSMenuEntryProviderI; import jalview.ws.jws2.jabaws2.Jws2Instance; +import jalview.ws.params.ParamDatastoreI; import java.awt.Color; import java.awt.event.ActionEvent; @@ -250,7 +251,11 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI services.add(service); // retrieve the presets and parameter set and cache now - service.getParamStore().getPresets(); + ParamDatastoreI pds = service.getParamStore(); + if (pds != null) + { + pds.getPresets(); + } service.hasParameters(); if (validServiceUrls == null) { diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java index 09f4a48..aa42ff7 100644 --- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java +++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java @@ -173,6 +173,8 @@ public class Jws2Instance : null)); } catch (Exception ex) { + System.err.println("Unexpected exception creating JabaParamStore."); + ex.printStackTrace(); } }