X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=35c78603080e3610f3b108d347660bb3223267c2;hb=0f61ed3a492c115c5047fc862104111d83b62256;hp=d829d020a0d1d8af830619b6f36b7508933cab33;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index d829d02..35c7860 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -1,25 +1,25 @@
-/*******************************************************************************
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
* This file is part of Jalview.
- *
+ *
* Jalview 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 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview 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 Jalview. If not, see
- * ['mouseover',String(pdb file URI), String(pdb file chain ID), String(residue + * ['mouseover',String(pdb file URI), String(pdb file chain ID), String(residue * number moused over), String(atom index corresponding to residue)] ** @@ -49,8 +54,8 @@ import jalview.structure.StructureSelectionManager; *
- * ['colourstruct',String(alignment view id),String(number of javascript message - * chunks to collect),String(length of first chunk in set of messages - or zero + * ['colourstruct',String(alignment view id),String(number of javascript message + * chunks to collect),String(length of first chunk in set of messages - or zero * for null message)] ** @@ -83,54 +88,49 @@ public class MouseOverStructureListener extends JSFunctionExec implements { for (int i = 0; i < modelSet.length; i++) { - // resolve a real filename - try - { - if (new java.net.URL(modelSet[i]).openConnection() != null) - { - continue; - } - } catch (Exception x) - { - } - ; - try - { - String db = jvlite.getDocumentBase().toString(); - db = db.substring(0, db.lastIndexOf("/")); - if (new java.net.URL(db + "/" + modelSet[i]).openConnection() != null) - { - modelSet[i] = db + "/" + modelSet[i]; - continue; - } - } catch (Exception x) - { - } - ; - try - { - if (new java.net.URL(jvlite.getCodeBase() + modelSet[i]) - .openConnection() != null) - { - modelSet[i] = jvlite.getCodeBase() + modelSet[i]; - continue; - } - } catch (Exception x) - { - } - ; - + modelSet[i] = resolveModelFile(modelSet[i]); } } } + /** + * Returns the first out of: file, file prefixed by document base, or file + * prefixed by codebase which can be resolved to a valid URL. If none can, + * returns the input parameter value. + * + * @param file + */ + public String resolveModelFile(String file) + { + // TODO reuse JalviewLite.LoadingThread.addProtocol instead + if (HttpUtils.isValidUrl(file)) + { + return file; + } + + String db = jvlite.getDocumentBase().toString(); + db = db.substring(0, db.lastIndexOf("/")); + String docBaseFile = db + "/" + file; + if (HttpUtils.isValidUrl(docBaseFile)) + { + return docBaseFile; + } + + String cb = jvlite.getCodeBase() + file; + if (HttpUtils.isValidUrl(cb)) + { + return cb; + } + + return file; + } + @Override public String[] getPdbFile() { return modelSet; } - @Override public void mouseOverStructure(int atomIndex, String strInfo) { @@ -141,24 +141,27 @@ public class MouseOverStructureListener extends JSFunctionExec implements } @Override - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbId) + public void highlightAtoms(List