JAL-4121 Added a NPE check caught in tests. Added --gui to relevant tests.

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 24320b5..563f0e7 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -53,6 +53,7 @@ import jalview.gui.IProgressIndicator;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings.TFType;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -326,7 +327,7 @@ public class StructureSelectionManager
           IProgressIndicator progress)
   {
     return computeMapping(true, sequence, targetChains, pdbFile, protocol,
-            progress);
+            progress, null, null, true);
   }
 
   /**
@@ -349,10 +350,20 @@ public class StructureSelectionManager
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
-          String pdbFile, DataSourceType sourceType)
+          String pdbFile, DataSourceType sourceType, TFType tft,
+          String paeFilename)
+  {
+    return setMapping(forStructureView, sequenceArray, targetChainIds,
+            pdbFile, sourceType, tft, paeFilename, true);
+  }
+
+  synchronized public StructureFile setMapping(boolean forStructureView,
+          SequenceI[] sequenceArray, String[] targetChainIds,
+          String pdbFile, DataSourceType sourceType, TFType tft,
+          String paeFilename, boolean doXferSettings)
   {
     return computeMapping(forStructureView, sequenceArray, targetChainIds,
-            pdbFile, sourceType, null);
+            pdbFile, sourceType, null, tft, paeFilename, doXferSettings);
   }
 
   /**
@@ -382,7 +393,8 @@ public class StructureSelectionManager
   synchronized public StructureFile computeMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
           String pdbFile, DataSourceType sourceType,
-          IProgressIndicator progress)
+          IProgressIndicator progress, TFType tft, String paeFilename,
+          boolean doXferSettings)
   {
     long progressSessionId = System.currentTimeMillis() * 3;
 
@@ -392,8 +404,7 @@ public class StructureSelectionManager
     // FIXME: possibly should just delete
 
     boolean parseSecStr = processSecondaryStructure
-            ? isStructureFileProcessed(pdbFile, sequenceArray)
-            : false;
+            && !isStructureFileProcessed(pdbFile, sequenceArray);
 
     StructureFile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
@@ -402,10 +413,19 @@ public class StructureSelectionManager
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
       pdb = new JmolParser(false, pdbFile, sourceType);
+      if (paeFilename != null)
+      {
+        pdb.setPAEMatrix(paeFilename);
+      }
+      pdb.setTemperatureFactorType(tft);
       pdb.addSettings(parseSecStr && processSecondaryStructure,
               parseSecStr && addTempFacAnnot,
               parseSecStr && secStructServices);
+      // save doXferSettings and reset after doParse()
+      boolean temp = pdb.getDoXferSettings();
+      pdb.setDoXferSettings(doXferSettings);
       pdb.doParse();
+      pdb.setDoXferSettings(temp);
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)
       {
@@ -660,7 +680,7 @@ public class StructureSelectionManager
   private boolean isStructureFileProcessed(String pdbFile,
           SequenceI[] sequenceArray)
   {
-    boolean parseSecStr = true;
+    boolean processed = false;
     if (isPDBFileRegistered(pdbFile))
     {
       for (SequenceI sq : sequenceArray)
@@ -680,13 +700,13 @@ public class StructureSelectionManager
             // passed, not the structure data ID -
             if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
             {
-              parseSecStr = false;
+              processed = true;
             }
           }
         }
       }
     }
-    return parseSecStr;
+    return processed;
   }
 
   public void addStructureMapping(StructureMapping sm)
@@ -1594,4 +1614,14 @@ public class StructureSelectionManager
     }
   }
 
+  public Map<String, String> getPdbFileNameIdMap()
+  {
+    return pdbFileNameId;
+  }
+
+  public Map<String, String> getPdbIdFileNameMap()
+  {
+    return pdbIdFileName;
+  }
+
 }