X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureChooser.java;h=5cd339b2a4e760c05b093af796cdf16b45dd7654;hb=f3d6a13271e3f34dfb4e40d6a2a7df1d392f8014;hp=0823652ea51b1c3b3649c36defdd9ef9b57f0e8c;hpb=2ee5edd84da7c509efc15d241527fa62093b41c7;p=jalview.git

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 0823652..5cd339b 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -25,7 +25,6 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.io.File;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
@@ -44,15 +43,15 @@ import javax.swing.JTable;
 import javax.swing.SwingUtilities;
 import javax.swing.table.AbstractTableModel;
 
-import org.json.simple.parser.ParseException;
+import com.stevesoft.pat.Regex;
 
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolParser;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
@@ -65,9 +64,9 @@ 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.io.StructureFile;
 import jalview.jbgui.FilterOption;
 import jalview.jbgui.GStructureChooser;
 import jalview.structure.StructureImportSettings.TFType;
@@ -78,6 +77,7 @@ 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;
@@ -688,8 +688,9 @@ public class StructureChooser extends GStructureChooser
       boolean guessTFType = localPdbPaeMatrixFileName == null;
       localPdbPaeMatrixFileName = guessPAEFilename();
       guessTFType |= localPdbPaeMatrixFileName != null;
+      Regex alphaFold = JmolParser.getNewAlphafoldValidator();
       if (guessTFType
-              && new File(selectedPdbFileName).getName().startsWith("AF-")
+              && alphaFold.search(new File(selectedPdbFileName).getName())
               && !tempFacAsChanged)
       {
         // localPdbPaeMatrixFileName was null and now isn't and filename could
@@ -701,7 +702,7 @@ public class StructureChooser extends GStructureChooser
   }
 
   /**
-   * Handles action event for btn_pdbFromFile
+   * Handles action event for btn_paeMatrixFile
    */
   @Override
   protected void paeMatrixFile_actionPerformed()
@@ -730,10 +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();
@@ -1055,11 +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");
@@ -1184,7 +1201,13 @@ public class StructureChooser extends GStructureChooser
     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 
     final int preferredHeight = pnl_filter.getHeight();
-
+    btn_add.setEnabled(false);
+    btn_newView.setEnabled(false);
+    btn_cancel.setEnabled(false);
+    actionsPanel.setEnabled(false);
+    
+    final String progress=MessageManager.getString("label.working_ellipsis");
+    setProgressBar(progress, progress.hashCode());
     Runnable viewStruc = new Runnable()
     {
       @Override
@@ -1268,62 +1291,27 @@ public class StructureChooser extends GStructureChooser
         }
         else if (currentView == VIEWS_FROM_FILE)
         {
-
-          // TEMPFAC NOT WORKING
-          TFType tft = (TFType) StructureChooser.this.combo_tempFacAs
-                  .getSelectedItem();
-          if (tft != null && tft != TFType.DEFAULT)
-          {
-            ssm.setAddTempFacAnnot(true);
-          }
-
+          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();
           if (userSelectedSeq != null)
           {
             selectedSequence = userSelectedSeq;
           }
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(selectedPdbFileName,
-                          DataSourceType.FILE, selectedSequence, true,
-                          Desktop.instance);
-
-          List<SequenceI> seqList = new ArrayList<>();
-          seqList.add(selectedSequence);
-          SequenceI[] seqArray = new SequenceI[] { selectedSequence };
-          StructureFile sf = ssm.computeMapping(true, seqArray, null,
-                  selectedPdbFileName, DataSourceType.FILE, null);
-          // EBIAlfaFold.addAlphaFoldPAEToStructure(pdbAlignment, pae, index,
-          // structIdOrFile, isStructId);
-          StructureMapping[] sm = ssm.getMapping(fileEntry.getFile());
-          // DO SOMETHING WITH
-          String paeFilename = StructureChooser.this.localPdbPaeMatrixFileName;
-          File paeFile = paeFilename == null ? null : new File(paeFilename);
-          if (paeFilename != null && paeFile.exists())
-          {
-            AlignmentI al = StructureChooser.this.ap.getAlignment();
-            try
-            {
-              EBIAlfaFold.importPaeJSONAsContactMatrixToSequence(al,
-                      paeFile, -1, selectedSequence.getName());
-            } catch (IOException | ParseException e)
-            {
-              // TODO Auto-generated catch block
-              e.printStackTrace();
-            }
-          }
+          String pdbFilename = selectedPdbFileName;
 
-          sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
-                  ap, new SequenceI[]
-                  { selectedSequence });
+          StructureChooser.openStructureFileForSequence(ssm, sc, ap,
+                  selectedSequence, true, pdbFilename, tft, paeFilename);
         }
         SwingUtilities.invokeLater(new Runnable()
         {
           @Override
           public void run()
           {
+            setProgressBar("Complete.", progress.hashCode());
             closeAction(preferredHeight);
             mainFrame.dispose();
           }
@@ -1447,6 +1435,7 @@ public class StructureChooser extends GStructureChooser
       setProgressBar(MessageManager.formatMessage(
               "status.fetching_3d_structures_for",
               pdbEntriesToView[0].getId()), progressId);
+      // Can we pass a pre-computeMappinged pdbFile?
       theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
     }
     setProgressBar(null, progressId);
@@ -1745,30 +1734,29 @@ 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();
   }
 }