X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=8168ce12fb9f653f03ffa504a9ecc134da925cc6;hb=c4b90e7ff57436d6bb96d316eed24c887b241f4d;hp=962dc0d1bef1f8d4ed2f9891cf0ddcb9b4447505;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 962dc0d..8168ce1 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -32,6 +32,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
@@ -180,13 +181,13 @@ public class Jalview2XML
    * Map of reconstructed AlignFrame objects that appear to have come from
    * SplitFrame objects (have a dna/protein complement view).
    */
-  private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<Viewport, AlignFrame>();
+  private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
 
   /*
    * Map from displayed rna structure models to their saved session state jar
    * entry names
    */
-  private Map<RnaModel, String> rnaSessions = new HashMap<RnaModel, String>();
+  private Map<RnaModel, String> rnaSessions = new HashMap<>();
 
   /**
    * create/return unique hash string for sq
@@ -247,19 +248,19 @@ public class Jalview2XML
   {
     if (seqsToIds == null)
     {
-      seqsToIds = new IdentityHashMap<SequenceI, String>();
+      seqsToIds = new IdentityHashMap<>();
     }
     if (seqRefIds == null)
     {
-      seqRefIds = new HashMap<String, SequenceI>();
+      seqRefIds = new HashMap<>();
     }
     if (incompleteSeqs == null)
     {
-      incompleteSeqs = new HashMap<String, SequenceI>();
+      incompleteSeqs = new HashMap<>();
     }
     if (frefedSequence == null)
     {
-      frefedSequence = new ArrayList<SeqFref>();
+      frefedSequence = new ArrayList<>();
     }
   }
 
@@ -458,9 +459,9 @@ public class Jalview2XML
    * This maintains a map of viewports, the key being the seqSetId. Important to
    * set historyItem and redoList for multiple views
    */
-  Map<String, AlignViewport> viewportsAdded = new HashMap<String, AlignViewport>();
+  Map<String, AlignViewport> viewportsAdded = new HashMap<>();
 
-  Map<String, AlignmentAnnotation> annotationIds = new HashMap<String, AlignmentAnnotation>();
+  Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
 
   String uniqueSetSuffix = "";
 
@@ -536,7 +537,7 @@ public class Jalview2XML
    */
   private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
   {
-    Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
+    Hashtable<String, AlignFrame> dsses = new Hashtable<>();
 
     /*
      * ensure cached data is clear before starting
@@ -551,8 +552,8 @@ public class Jalview2XML
       // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
       // //////////////////////////////////////////////////
 
-      List<String> shortNames = new ArrayList<String>();
-      List<String> viewIds = new ArrayList<String>();
+      List<String> shortNames = new ArrayList<>();
+      List<String> viewIds = new ArrayList<>();
 
       // REVERSE ORDER
       for (int i = frames.size() - 1; i > -1; i--)
@@ -662,7 +663,7 @@ public class Jalview2XML
     {
       FileOutputStream fos = new FileOutputStream(jarFile);
       JarOutputStream jout = new JarOutputStream(fos);
-      List<AlignFrame> frames = new ArrayList<AlignFrame>();
+      List<AlignFrame> frames = new ArrayList<>();
 
       // resolve splitframes
       if (af.getViewport().getCodingComplement() != null)
@@ -748,12 +749,12 @@ public class Jalview2XML
   {
     if (viewIds == null)
     {
-      viewIds = new ArrayList<String>();
+      viewIds = new ArrayList<>();
     }
 
     initSeqRefs();
 
-    List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
+    List<UserColourScheme> userColours = new ArrayList<>();
 
     AlignViewport av = ap.av;
     ViewportRanges vpRanges = av.getRanges();
@@ -807,9 +808,9 @@ public class Jalview2XML
     }
 
     JSeq jseq;
-    Set<String> calcIdSet = new HashSet<String>();
+    Set<String> calcIdSet = new HashSet<>();
     // record the set of vamsas sequence XML POJO we create.
-    HashMap<String, Sequence> vamsasSetIds = new HashMap<String, Sequence>();
+    HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
     // SAVE SEQUENCES
     for (final SequenceI jds : rjal.getSequences())
     {
@@ -882,48 +883,43 @@ public class Jalview2XML
 
       // TODO: omit sequence features from each alignment view's XML dump if we
       // are storing dataset
-      if (jds.getSequenceFeatures() != null)
+      List<jalview.datamodel.SequenceFeature> sfs = jds
+              .getSequenceFeatures();
+      for (SequenceFeature sf : sfs)
       {
-        jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures();
-        int index = 0;
-        while (index < sf.length)
-        {
-          Features features = new Features();
+        Features features = new Features();
 
-          features.setBegin(sf[index].getBegin());
-          features.setEnd(sf[index].getEnd());
-          features.setDescription(sf[index].getDescription());
-          features.setType(sf[index].getType());
-          features.setFeatureGroup(sf[index].getFeatureGroup());
-          features.setScore(sf[index].getScore());
-          if (sf[index].links != null)
+        features.setBegin(sf.getBegin());
+        features.setEnd(sf.getEnd());
+        features.setDescription(sf.getDescription());
+        features.setType(sf.getType());
+        features.setFeatureGroup(sf.getFeatureGroup());
+        features.setScore(sf.getScore());
+        if (sf.links != null)
+        {
+          for (int l = 0; l < sf.links.size(); l++)
           {
-            for (int l = 0; l < sf[index].links.size(); l++)
-            {
-              OtherData keyValue = new OtherData();
-              keyValue.setKey("LINK_" + l);
-              keyValue.setValue(sf[index].links.elementAt(l).toString());
-              features.addOtherData(keyValue);
-            }
+            OtherData keyValue = new OtherData();
+            keyValue.setKey("LINK_" + l);
+            keyValue.setValue(sf.links.elementAt(l).toString());
+            features.addOtherData(keyValue);
           }
-          if (sf[index].otherDetails != null)
+        }
+        if (sf.otherDetails != null)
+        {
+          String key;
+          Iterator<String> keys = sf.otherDetails.keySet().iterator();
+          while (keys.hasNext())
           {
-            String key;
-            Iterator<String> keys = sf[index].otherDetails.keySet()
-                    .iterator();
-            while (keys.hasNext())
-            {
-              key = keys.next();
-              OtherData keyValue = new OtherData();
-              keyValue.setKey(key);
-              keyValue.setValue(sf[index].otherDetails.get(key).toString());
-              features.addOtherData(keyValue);
-            }
+            key = keys.next();
+            OtherData keyValue = new OtherData();
+            keyValue.setKey(key);
+            keyValue.setValue(sf.otherDetails.get(key).toString());
+            features.addOtherData(keyValue);
           }
-
-          jseq.addFeatures(features);
-          index++;
         }
+
+        jseq.addFeatures(features);
       }
 
       if (jdatasq.getAllPDBEntries() != null)
@@ -986,7 +982,7 @@ public class Jalview2XML
             pdb.setFile(matchedFile); // entry.getFile());
             if (pdbfiles == null)
             {
-              pdbfiles = new ArrayList<String>();
+              pdbfiles = new ArrayList<>();
             }
 
             if (!pdbfiles.contains(pdbId))
@@ -1107,7 +1103,7 @@ public class Jalview2XML
               Tree tree = new Tree();
               tree.setTitle(tp.getTitle());
               tree.setCurrentTree((av.currentTree == tp.getTree()));
-              tree.setNewick(tp.getTree().toString());
+              tree.setNewick(tp.getTree().print());
               tree.setThreshold(tp.treeCanvas.threshold);
 
               tree.setFitToWindow(tp.fitToWindow.getState());
@@ -1135,7 +1131,7 @@ public class Jalview2XML
     /**
      * store forward refs from an annotationRow to any groups
      */
-    IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<SequenceGroup, String>();
+    IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
     if (storeDS)
     {
       for (SequenceI sq : jal.getSequences())
@@ -1349,7 +1345,7 @@ public class Jalview2XML
                 .getFeatureRenderer().getRenderOrder()
                 .toArray(new String[0]);
 
-        Vector<String> settingsAdded = new Vector<String>();
+        Vector<String> settingsAdded = new Vector<>();
         if (renderOrder != null)
         {
           for (String featureType : renderOrder)
@@ -1392,7 +1388,7 @@ public class Jalview2XML
         // is groups actually supposed to be a map here ?
         Iterator<String> en = ap.getSeqPanel().seqCanvas
                 .getFeatureRenderer().getFeatureGroups().iterator();
-        Vector<String> groupsAdded = new Vector<String>();
+        Vector<String> groupsAdded = new Vector<>();
         while (en.hasNext())
         {
           String grp = en.next();
@@ -1415,17 +1411,16 @@ public class Jalview2XML
       {
         jalview.datamodel.HiddenColumns hidden = av.getAlignment()
                 .getHiddenColumns();
-        if (hidden == null || hidden.getListOfCols() == null)
+        if (hidden == null)
         {
           warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
         }
         else
         {
-          for (int c = 0; c < hidden.getListOfCols()
-                  .size(); c++)
+          ArrayList<int[]> hiddenRegions = hidden
+                  .getHiddenColumnsCopy();
+          for (int[] region : hiddenRegions)
           {
-            int[] region = hidden.getListOfCols()
-                    .get(c);
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);
@@ -2290,7 +2285,7 @@ public class Jalview2XML
     try
     {
       // create list to store references for any new Jmol viewers created
-      newStructureViewers = new Vector<JalviewStructureDisplayI>();
+      newStructureViewers = new Vector<>();
       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       // Workaround is to make sure caller implements the JarInputStreamProvider
       // interface
@@ -2383,8 +2378,8 @@ public class Jalview2XML
       initSeqRefs();
     }
     AlignFrame af = null, _af = null;
-    IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
-    Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
+    IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
+    Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
     final String file = jprovider.getFilename();
     try
     {
@@ -2525,9 +2520,9 @@ public class Jalview2XML
    */
   protected void restoreSplitFrames()
   {
-    List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
-    List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
-    Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
+    List<SplitFrame> gatherTo = new ArrayList<>();
+    List<AlignFrame> addedToSplitFrames = new ArrayList<>();
+    Map<String, AlignFrame> dna = new HashMap<>();
 
     /*
      * Identify the DNA alignments
@@ -2669,7 +2664,7 @@ public class Jalview2XML
     errorMessage = null;
   }
 
-  Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
+  Map<String, String> alreadyLoadedPDB = new HashMap<>();
 
   /**
    * when set, local views will be updated from view stored in JalviewXML
@@ -2840,7 +2835,7 @@ public class Jalview2XML
 
     List<SequenceI> hiddenSeqs = null;
 
-    List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
+    List<SequenceI> tmpseqs = new ArrayList<>();
 
     boolean multipleView = false;
     SequenceI referenceseqForView = null;
@@ -2908,7 +2903,7 @@ public class Jalview2XML
       {
         if (hiddenSeqs == null)
         {
-          hiddenSeqs = new ArrayList<SequenceI>();
+          hiddenSeqs = new ArrayList<>();
         }
 
         hiddenSeqs.add(tmpSeq);
@@ -2986,12 +2981,11 @@ public class Jalview2XML
           Features[] features = jseqs[i].getFeatures();
           for (int f = 0; f < features.length; f++)
           {
-            jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
-                    features[f].getType(), features[f].getDescription(),
-                    features[f].getStatus(), features[f].getBegin(),
-                    features[f].getEnd(), features[f].getFeatureGroup());
-
-            sf.setScore(features[f].getScore());
+            SequenceFeature sf = new SequenceFeature(features[f].getType(),
+                    features[f].getDescription(), features[f].getBegin(),
+                    features[f].getEnd(), features[f].getScore(),
+                    features[f].getFeatureGroup());
+            sf.setStatus(features[f].getStatus());
             for (int od = 0; od < features[f].getOtherDataCount(); od++)
             {
               OtherData keyValue = features[f].getOtherData(od);
@@ -3116,12 +3110,12 @@ public class Jalview2XML
 
     // ////////////////////////////////
     // LOAD ANNOTATIONS
-    List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
+    List<JvAnnotRow> autoAlan = new ArrayList<>();
 
     /*
      * store any annotations which forward reference a group's ID
      */
-    Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, List<AlignmentAnnotation>>();
+    Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
 
     if (vamsasSet.getAnnotationCount() > 0)
     {
@@ -3276,7 +3270,7 @@ public class Jalview2XML
                   .get(an[i].getGroupRef());
           if (aal == null)
           {
-            aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
+            aal = new ArrayList<>();
             groupAnnotRefs.put(an[i].getGroupRef(), aal);
           }
           aal.add(jaa);
@@ -3366,7 +3360,7 @@ public class Jalview2XML
         }
         int pidThreshold = jGroup.getPidThreshold();
 
-        Vector<SequenceI> seqs = new Vector<SequenceI>();
+        Vector<SequenceI> seqs = new Vector<>();
 
         for (int s = 0; s < jGroup.getSeqCount(); s++)
         {
@@ -3681,7 +3675,7 @@ public class Jalview2XML
         TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
         if (tp == null)
         {
-          tp = af.ShowNewickTree(
+          tp = af.showNewickTree(
                   new jalview.io.NewickFile(tree.getNewick()),
                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
                   tree.getXpos(), tree.getYpos());
@@ -3759,7 +3753,7 @@ public class Jalview2XML
      * Run through all PDB ids on the alignment, and collect mappings between
      * distinct view ids and all sequences referring to that view.
      */
-    Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
+    Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
 
     for (int i = 0; i < jseqs.length; i++)
     {
@@ -3957,8 +3951,8 @@ public class Jalview2XML
 
     Set<Entry<File, StructureData>> fileData = data.getFileData()
             .entrySet();
-    List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
-    List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
+    List<PDBEntry> pdbs = new ArrayList<>();
+    List<SequenceI[]> allseqs = new ArrayList<>();
     for (Entry<File, StructureData> pdb : fileData)
     {
       String filePath = pdb.getValue().getFilePath();
@@ -4014,9 +4008,9 @@ public class Jalview2XML
               getViewerJarEntryName(svattrib.getViewId()));
     }
 
-    List<String> pdbfilenames = new ArrayList<String>();
-    List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
-    List<String> pdbids = new ArrayList<String>();
+    List<String> pdbfilenames = new ArrayList<>();
+    List<SequenceI[]> seqmaps = new ArrayList<>();
+    List<String> pdbids = new ArrayList<>();
     StringBuilder newFileLoc = new StringBuilder(64);
     int cp = 0, ncp, ecp;
     Map<File, StructureData> oldFiles = svattrib.getFileData();
@@ -4464,7 +4458,7 @@ public class Jalview2XML
     af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
             .isShowUnconserved() : false);
     af.viewport.getRanges().setStartRes(view.getStartRes());
-    af.viewport.getRanges().setStartSeq(view.getStartSeq());
+    // startSeq set in af.alignPanel.updateLayout below
     af.alignPanel.updateLayout();
     ColourSchemeI cs = null;
     // apply colourschemes
@@ -4577,8 +4571,8 @@ public class Jalview2XML
       af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
-      Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
-      Map<String, Float> featureOrder = new Hashtable<String, Float>();
+      Map<String, FeatureColourI> featureColours = new Hashtable<>();
+      Map<String, Float> featureOrder = new Hashtable<>();
 
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
       {
@@ -4637,7 +4631,7 @@ public class Jalview2XML
           fdi.setVisible(setting.getType());
         }
       }
-      Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
+      Map<String, Boolean> fgtable = new Hashtable<>();
       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
       {
         Group grp = jms.getFeatureSettings().getGroup(gs);
@@ -4830,7 +4824,7 @@ public class Jalview2XML
       String[] magicNames = new String[] { "Consensus", "Quality",
           "Conservation" };
       JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
-      Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
+      Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
       for (String nm : magicNames)
       {
         visan.put(nm, nullAnnot);
@@ -4842,11 +4836,11 @@ public class Jalview2XML
                         + auan.template.getCalcId()), auan);
       }
       int hSize = al.getAlignmentAnnotation().length;
-      List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+      List<JvAnnotRow> reorder = new ArrayList<>();
       // work through any autoCalculated annotation already on the view
       // removing it if it should be placed in a different location on the
       // annotation panel.
-      List<String> remains = new ArrayList<String>(visan.keySet());
+      List<String> remains = new ArrayList<>(visan.keySet());
       for (int h = 0; h < hSize; h++)
       {
         jalview.datamodel.AlignmentAnnotation jalan = al
@@ -5174,7 +5168,7 @@ public class Jalview2XML
   {
     if (datasetIds == null)
     {
-      datasetIds = new Hashtable<String, AlignmentI>();
+      datasetIds = new Hashtable<>();
       return null;
     }
     if (datasetIds.containsKey(datasetId))
@@ -5188,7 +5182,7 @@ public class Jalview2XML
   {
     if (datasetIds == null)
     {
-      datasetIds = new Hashtable<String, AlignmentI>();
+      datasetIds = new Hashtable<>();
     }
     datasetIds.put(datasetId, dataset);
   }
@@ -5211,7 +5205,7 @@ public class Jalview2XML
       // make a new datasetId and record it
       if (dataset2Ids == null)
       {
-        dataset2Ids = new IdentityHashMap<AlignmentI, String>();
+        dataset2Ids = new IdentityHashMap<>();
       }
       else
       {
@@ -5490,11 +5484,11 @@ public class Jalview2XML
         // register sequence object so the XML parser can recover it.
         if (seqRefIds == null)
         {
-          seqRefIds = new HashMap<String, SequenceI>();
+          seqRefIds = new HashMap<>();
         }
         if (seqsToIds == null)
         {
-          seqsToIds = new IdentityHashMap<SequenceI, String>();
+          seqsToIds = new IdentityHashMap<>();
         }
         seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
         seqsToIds.put((SequenceI) jvobj, id);