JAL-4177 disable add/new view when an import is started.

[jalview.git] / src / jalview / gui / StructureChooser.java

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 80024d9..4e5378e 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -64,6 +64,7 @@ import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
 import jalview.gui.structurechooser.StructureChooserQuerySource;
 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
 import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.FilterOption;
@@ -76,6 +77,8 @@ import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.sifts.SiftsSettings;
 
@@ -699,7 +702,7 @@ public class StructureChooser extends GStructureChooser
   }
 
   /**
-   * Handles action event for btn_pdbFromFile
+   * Handles action event for btn_paeMatrixFile
    */
   @Override
   protected void paeMatrixFile_actionPerformed()
@@ -728,10 +731,24 @@ public class StructureChooser extends GStructureChooser
             "label.load_pae_matrix_file_associate_with_structure",
             pdbFile.getName()));
 
+    // TODO convert to Callable/Promise
     int value = chooser.showOpenDialog(null);
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      localPdbPaeMatrixFileName = chooser.getSelectedFile().getPath();
+      String fileName = chooser.getSelectedFile().getPath();
+      try {
+        PAEContactMatrix.validateContactMatrixFile(fileName);
+      } catch (Exception thr)
+      {
+        JvOptionPane.showInternalMessageDialog(this, MessageManager
+                .formatMessage("label.couldnt_load_file", new Object[]
+                { fileName})+"<br>"+thr.getLocalizedMessage(),
+                MessageManager.getString("label.error_loading_file"),
+                JvOptionPane.WARNING_MESSAGE);
+        Console.error("Couldn't import "+fileName+" as a PAE matrix",thr);
+        return;
+      }
+      localPdbPaeMatrixFileName = fileName;
       Cache.setProperty("LAST_DIRECTORY", localPdbPaeMatrixFileName);
     }
     validateAssociationFromFile();
@@ -1053,11 +1070,13 @@ public class StructureChooser extends GStructureChooser
       {
         pdbFileString = MessageManager.getString("label.none");
         pdbFileTooltip = MessageManager.getString("label.nothing_selected");
+        setPdbOptionsEnabled(false);
       }
     }
     else
     {
       btn_pdbFromFile.setEnabled(false);
+      setPdbOptionsEnabled(false);
       // lbl_fromFileStatus.setIcon(errorImage);
       pdbFileString = MessageManager.getString("label.none");
       pdbFileTooltip = MessageManager.getString("label.nothing_selected");
@@ -1182,7 +1201,8 @@ public class StructureChooser extends GStructureChooser
     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 
     final int preferredHeight = pnl_filter.getHeight();
-
+    btn_add.setEnabled(false);
+    btn_newView.setEnabled(false);
     Runnable viewStruc = new Runnable()
     {
       @Override
@@ -1266,9 +1286,9 @@ public class StructureChooser extends GStructureChooser
         }
         else if (currentView == VIEWS_FROM_FILE)
         {
-          TFType tft = (TFType) StructureChooser.this.combo_tempFacAs
-                  .getSelectedItem();
-          String paeFilename = StructureChooser.this.localPdbPaeMatrixFileName;
+          StructureChooser sc = StructureChooser.this;
+          TFType tft = (TFType) sc.combo_tempFacAs.getSelectedItem();
+          String paeFilename = sc.localPdbPaeMatrixFileName;
           AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
                   .getCmb_assSeq().getSelectedItem();
           SequenceI userSelectedSeq = assSeqOpt.getSequence();
@@ -1276,37 +1296,8 @@ public class StructureChooser extends GStructureChooser
             selectedSequence = userSelectedSeq;
           String pdbFilename = selectedPdbFileName;
 
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(pdbFilename, DataSourceType.FILE,
-                          selectedSequence, true, Desktop.instance, tft,
-                          paeFilename);
-
-          /*
-          SequenceI[] seqArray = new SequenceI[] { selectedSequence };
-          
-          StructureFile sf = ssm.computeMapping(true, seqArray, null,
-                  selectedPdbFileName, DataSourceType.FILE, null, tft,
-                  paeFilename);
-          StructureMapping[] sm = ssm.getMapping(fileEntry.getFile());
-          // DO SOMETHING WITH
-          File paeFile = paeFilename == null ? null : new File(paeFilename);
-          if (paeFilename != null && paeFile.exists())
-          {
-            AlignmentI al = StructureChooser.this.ap.getAlignment();
-            try
-            {
-              EBIAlfaFold.importPaeJSONAsContactMatrixToSequence(al,
-                      paeFile, selectedSequence);
-            } catch (IOException | ParseException e)
-            {
-              // TODO Auto-generated catch block
-              e.printStackTrace();
-            }
-          }
-          */
-          sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
-                  ap, new SequenceI[]
-                  { selectedSequence });
+          StructureChooser.openStructureFileForSequence(ssm, sc, ap,
+                  selectedSequence, true, pdbFilename, tft, paeFilename);
         }
         SwingUtilities.invokeLater(new Runnable()
         {
@@ -1735,30 +1726,29 @@ public class StructureChooser extends GStructureChooser
   /**
    * Open a single structure file for a given sequence
    */
-  public static void openStructureFileForSequence(AlignmentPanel ap,
-          SequenceI seq, File sFile)
+  public static void openStructureFileForSequence(
+          StructureSelectionManager ssm, StructureChooser sc,
+          AlignmentPanel ap, SequenceI seq, boolean prompt,
+          String sFilename, TFType tft, String paeFilename)
   {
-    // Open the chooser headlessly. Not sure this is actually needed ?
-    StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq,
-            ap, false);
-    StructureSelectionManager ssm = ap.getStructureSelectionManager();
-    PDBEntry fileEntry = null;
-    try
-    {
-      fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
-              sFile.getAbsolutePath(), DataSourceType.FILE, seq, true,
-              Desktop.instance);
-    } catch (Exception e)
-    {
-      Console.error("Could not open structure file '"
-              + sFile.getAbsolutePath() + "'");
-      return;
+    boolean headless = false;
+    if (sc == null)
+    {
+      headless = true;
+      sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
     }
+    if (ssm == null)
+      ssm = ap.getStructureSelectionManager();
+
+    PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+            sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
+            tft, paeFilename);
 
     StructureViewer sViewer = sc.launchStructureViewer(ssm,
             new PDBEntry[]
             { fileEntry }, ap, new SequenceI[] { seq });
 
-    sc.mainFrame.dispose();
+    if (headless)
+      sc.mainFrame.dispose();
   }
 }