JAL-3626 reconciled Platform
[jalview.git] / src / jalview / project / Jalview2XML.java
index 1a25270..c28002f 100644 (file)
@@ -150,6 +150,7 @@ import jalview.xml.binding.jalview.ThresholdType;
 import jalview.xml.binding.jalview.VAMSAS;
 
 import java.awt.Color;
+import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
@@ -160,6 +161,7 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
@@ -265,6 +267,25 @@ public class Jalview2XML
   private Map<RnaModel, String> rnaSessions = new HashMap<>();
 
   /**
+   * contains last error message (if any) encountered by XML loader.
+   */
+  String errorMessage = null;
+
+  /**
+   * flag to control whether the Jalview2XML_V1 parser should be deferred to if
+   * exceptions are raised during project XML parsing
+   */
+  public boolean attemptversion1parse = false;
+
+  /*
+   * JalviewJS only -- to allow read file bytes to be saved in the
+   * created AlignFrame, allowing File | Reload of a project file to work
+   * 
+   * BH 2019 JAL-3436
+   */
+  private File jarFile;
+
+  /**
    * A helper method for safely using the value of an optional attribute that
    * may be null if not present in the XML. Answers the boolean value, or false
    * if null.
@@ -424,7 +445,7 @@ public class Jalview2XML
    * @param _jmap
    * @return
    */
-  public SeqFref newMappingRef(final String sref,
+  protected SeqFref newMappingRef(final String sref,
           final jalview.datamodel.Mapping _jmap)
   {
     SeqFref fref = new SeqFref(sref, "Mapping")
@@ -446,7 +467,7 @@ public class Jalview2XML
     return fref;
   }
 
-  public SeqFref newAlcodMapRef(final String sref,
+  protected SeqFref newAlcodMapRef(final String sref,
           final AlignedCodonFrame _cf,
           final jalview.datamodel.Mapping _jmap)
   {
@@ -478,7 +499,7 @@ public class Jalview2XML
     return fref;
   }
 
-  public void resolveFrefedSequences()
+  protected void resolveFrefedSequences()
   {
     Iterator<SeqFref> nextFref = frefedSequence.iterator();
     int toresolve = frefedSequence.size();
@@ -846,7 +867,7 @@ public class Jalview2XML
    * @param out
    *          jar entry name
    */
-  public JalviewModel saveState(AlignmentPanel ap, String fileName,
+  protected JalviewModel saveState(AlignmentPanel ap, String fileName,
           JarOutputStream jout, List<String> viewIds)
   {
     return saveState(ap, fileName, false, jout, viewIds);
@@ -868,7 +889,7 @@ public class Jalview2XML
    * @param out
    *          jar entry name
    */
-  public JalviewModel saveState(AlignmentPanel ap, String fileName,
+  protected JalviewModel saveState(AlignmentPanel ap, String fileName,
           boolean storeDS, JarOutputStream jout, List<String> viewIds)
   {
     if (viewIds == null)
@@ -2730,17 +2751,6 @@ public class Jalview2XML
   }
 
   /**
-   * contains last error message (if any) encountered by XML loader.
-   */
-  String errorMessage = null;
-
-  /**
-   * flag to control whether the Jalview2XML_V1 parser should be deferred to if
-   * exceptions are raised during project XML parsing
-   */
-  public boolean attemptversion1parse = false;
-
-  /**
    * Load a jalview project archive from a jar file
    * 
    * @param file
@@ -2788,55 +2798,55 @@ public class Jalview2XML
         System.err.println("Error loading alignment: " + x.getMessage());
       }
     }
+    this.jarFile = null;
     return af;
   }
 
        @SuppressWarnings("unused")
-       private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
-
-               // BH 2018 allow for bytes already attached to File object
-               try {
-                       String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
+  private jarInputStreamProvider createjarInputStreamProvider(
+          final Object ofile) throws MalformedURLException
+  {
+    try
+    {
+      String file = (ofile instanceof File
+              ? ((File) ofile).getCanonicalPath()
+              : ofile.toString());
       byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
               : null;
-                       URL url = null;
-                       errorMessage = null;
-                       uniqueSetSuffix = null;
-                       seqRefIds = null;
-                       viewportsAdded.clear();
-                       frefedSequence = null;
-
-                       if (file.startsWith("http://")) {
-                               url = new URL(file);
-                       }
-                       final URL _url = url;
-                       return new jarInputStreamProvider() {
-
-                               @Override
-                               public JarInputStream getJarInputStream() throws IOException {
-                                       if (bytes != null) {
-//                                             System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
-                                               return new JarInputStream(new ByteArrayInputStream(bytes));
-                                       }
-                                       if (_url != null) {
-//                                             System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
-                                               return new JarInputStream(_url.openStream());
-                                       } else {
-//                                             System.out.println("Jalview2XML: opening file jarInputStream for " + file);
-                                               return new JarInputStream(new FileInputStream(file));
-                                       }
-                               }
-
-                               @Override
-                               public String getFilename() {
-                                       return file;
-                               }
-                       };
-               } catch (IOException e) {
-                       e.printStackTrace();
-                       return null;
-               }
-       }
+      if (bytes != null)
+      {
+        this.jarFile = (File) ofile;
+      }
+      errorMessage = null;
+      uniqueSetSuffix = null;
+      seqRefIds = null;
+      viewportsAdded.clear();
+      frefedSequence = null;
+
+      URL url = file.startsWith("http://") ? new URL(file) : null;
+      return new jarInputStreamProvider()
+      {
+        @Override
+        public JarInputStream getJarInputStream() throws IOException
+        {
+          InputStream is = bytes != null ? new ByteArrayInputStream(bytes)
+                  : (url != null ? url.openStream()
+                          : new FileInputStream(file));
+          return new JarInputStream(is);
+        }
+
+        @Override
+        public String getFilename()
+        {
+          return file;
+        }
+      };
+    } catch (IOException e)
+    {
+      e.printStackTrace();
+      return null;
+    }
+  }
 
   /**
    * Recover jalview session from a jalview project archive. Caller may
@@ -4684,7 +4694,8 @@ public class Jalview2XML
           String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
           filedat = oldFiles.get(new File(reformatedOldFilename));
         }
-        newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
+        newFileLoc
+                .append(Platform.escapeBackslashes(filedat.getFilePath()));
         pdbfilenames.add(filedat.getFilePath());
         pdbids.add(filedat.getPdbId());
         seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
@@ -4996,27 +5007,28 @@ public class Jalview2XML
     }
   }
 
-  AlignFrame loadViewport(String file, List<JSeq> JSEQ,
-          List<SequenceI> hiddenSeqs, AlignmentI al,
-          JalviewModel jm, Viewport view, String uniqueSeqSetId,
-          String viewId, List<JvAnnotRow> autoAlan)
+  AlignFrame loadViewport(String fileName, List<JSeq> JSEQ,
+          List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+          Viewport view, String uniqueSeqSetId, String viewId,
+          List<JvAnnotRow> autoAlan)
   {
     AlignFrame af = null;
     af = new AlignFrame(al, safeInt(view.getWidth()),
             safeInt(view.getHeight()), uniqueSeqSetId, viewId)
-//    {
-//     
-//     @Override
-//     protected void processKeyEvent(java.awt.event.KeyEvent e) {
-//             System.out.println("Jalview2XML   AF " + e);
-//             super.processKeyEvent(e);
-//             
-//     }
-//     
-//    }
+    // {
+    //
+    // @Override
+    // protected void processKeyEvent(java.awt.event.KeyEvent e) {
+    // System.out.println("Jalview2XML AF " + e);
+    // super.processKeyEvent(e);
+    //
+    // }
+    //
+    // }
     ;
     af.alignPanel.setHoldRepaint(true);
-    af.setFileName(file, FileFormat.Jalview);
+    af.setFileName(fileName, FileFormat.Jalview);
+    af.setFileObject(jarFile); // BH 2019 JAL-3436
 
     final AlignViewport viewport = af.getViewport();
     for (int i = 0; i < JSEQ.size(); i++)
@@ -5091,9 +5103,8 @@ public class Jalview2XML
 
     viewport.setColourText(safeBoolean(view.isShowColourText()));
 
-    viewport
-            .setConservationSelected(
-                    safeBoolean(view.isConservationSelected()));
+    viewport.setConservationSelected(
+            safeBoolean(view.isConservationSelected()));
     viewport.setIncrement(safeInt(view.getConsThreshold()));
     viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
     viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
@@ -5179,9 +5190,8 @@ public class Jalview2XML
     af.changeColour(cs);
     viewport.setColourAppliesToAllGroups(true);
 
-    viewport
-            .setShowSequenceFeatures(
-                    safeBoolean(view.isShowSequenceFeatures()));
+    viewport.setShowSequenceFeatures(
+            safeBoolean(view.isShowSequenceFeatures()));
 
     viewport.setCentreColumnLabels(view.isCentreColumnLabels());
     viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
@@ -5202,13 +5212,13 @@ public class Jalview2XML
               .getFeatureRenderer();
       FeaturesDisplayed fdi;
       viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
-      String[] renderOrder = new String[jm.getFeatureSettings()
-              .getSetting().size()];
+      String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+              .size()];
       Map<String, FeatureColourI> featureColours = new Hashtable<>();
       Map<String, Float> featureOrder = new Hashtable<>();
 
-      for (int fs = 0; fs < jm.getFeatureSettings()
-              .getSetting().size(); fs++)
+      for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+              .size(); fs++)
       {
         Setting setting = jm.getFeatureSettings().getSetting().get(fs);
         String featureType = setting.getType();
@@ -5220,8 +5230,8 @@ public class Jalview2XML
                 .getMatcherSet();
         if (filters != null)
         {
-          FeatureMatcherSetI filter = Jalview2XML
-                  .parseFilter(featureType, filters);
+          FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+                  filters);
           if (!filter.isEmpty())
           {
             fr.setFeatureFilter(featureType, filter);
@@ -5253,8 +5263,7 @@ public class Jalview2XML
           float max = setting.getMax() == null ? 1f
                   : setting.getMax().floatValue();
           FeatureColourI gc = new FeatureColour(maxColour, minColour,
-                  maxColour,
-                  noValueColour, min, max);
+                  maxColour, noValueColour, min, max);
           if (setting.getAttributeName().size() > 0)
           {
             gc.setAttributeName(setting.getAttributeName().toArray(
@@ -5288,8 +5297,7 @@ public class Jalview2XML
         }
         else
         {
-          featureColours.put(featureType,
-                  new FeatureColour(maxColour));
+          featureColours.put(featureType, new FeatureColour(maxColour));
         }
         renderOrder[fs] = featureType;
         if (setting.getOrder() != null)
@@ -5357,8 +5365,9 @@ public class Jalview2XML
     String complementaryViewId = view.getComplementId();
     if (complementaryViewId == null)
     {
-      Desktop.addInternalFrame(af, view.getTitle(),
+      Dimension dim = Platform.getDimIfEmbedded(af,
               safeInt(view.getWidth()), safeInt(view.getHeight()));
+      Desktop.addInternalFrame(af, view.getTitle(), dim.width, dim.height);
       // recompute any autoannotation
       af.alignPanel.updateAnnotation(false, true);
       reorderAutoannotation(af, al, autoAlan);
@@ -5625,7 +5634,7 @@ public class Jalview2XML
     return false;
   }
 
-  public void addToSkipList(AlignFrame af)
+  protected void addToSkipList(AlignFrame af)
   {
     if (skipList == null)
     {
@@ -5634,7 +5643,7 @@ public class Jalview2XML
     skipList.put(af.getViewport().getSequenceSetId(), af);
   }
 
-  public void clearSkipList()
+  protected void clearSkipList()
   {
     if (skipList != null)
     {
@@ -6118,14 +6127,8 @@ public class Jalview2XML
     AlignFrame af = loadFromObject(jm, null, false, null);
     af.getAlignPanels().clear();
     af.closeMenuItem_actionPerformed(true);
-
-    /*
-     * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
-     * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
-     * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
-     * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
-     * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
-     */
+    af.alignPanel.setHoldRepaint(false);
+    this.jarFile = null;
 
     return af.alignPanel;
   }
@@ -6476,8 +6479,10 @@ public class Jalview2XML
                   axis.getXPos(), axis.getYPos(), axis.getZPos());
         }
 
+        Dimension dim = Platform.getDimIfEmbedded(panel, 475, 450);
         Desktop.addInternalFrame(panel, MessageManager.formatMessage(
-                "label.calc_title", "PCA", modelName), 475, 450);
+                "label.calc_title", "PCA", modelName), dim.width,
+                dim.height);
       }
     } catch (Exception ex)
     {