JAL-629 Adding PAE and TFType at structure loading time. Display PAE automatically

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 4a70bd9..5341874 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -14,7 +14,6 @@ import java.util.Map;
 import java.util.Map.Entry;
 
 import jalview.analysis.AlignmentUtils;
-import jalview.api.AlignmentViewPanel;
 import jalview.bin.argparser.Arg;
 import jalview.bin.argparser.ArgParser;
 import jalview.bin.argparser.ArgValue;
@@ -42,13 +41,11 @@ import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.schemes.AnnotationColourGradient;
-import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import jalview.ws.dbsources.EBIAlfaFold;
 import mc_view.PDBChain;
 
 public class Commands
@@ -245,44 +242,10 @@ public class Commands
            * ssm.setProcessSecondaryStructure(showSecondaryStructure); }
            */
 
-          // get kind of temperature factor annotation
-          StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
-          if ((!avm.getBoolean(Arg.NOTEMPFAC))
-                  && avm.containsArg(Arg.TEMPFAC))
-          {
-            try
-            {
-              tempfacType = StructureImportSettings.TFType
-                      .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
-                              .toUpperCase(Locale.ROOT));
-              Console.debug("Obtained Temperature Factor type of '"
-                      + tempfacType + "'");
-            } catch (IllegalArgumentException e)
-            {
-              // Just an error message!
-              StringBuilder sb = new StringBuilder().append("Cannot set ")
-                      .append(Arg.TEMPFAC.argString()).append(" to '")
-                      .append(tempfacType)
-                      .append("', ignoring.  Valid values are: ");
-              Iterator<StructureImportSettings.TFType> it = Arrays
-                      .stream(StructureImportSettings.TFType.values())
-                      .iterator();
-              while (it.hasNext())
-              {
-                sb.append(it.next().toString().toLowerCase(Locale.ROOT));
-                if (it.hasNext())
-                  sb.append(", ");
-              }
-              Console.warn(sb.toString());
-            }
-          }
-
           Console.debug(
                   "Opening '" + openFile + "' in new alignment frame");
           FileLoader fileLoader = new FileLoader(!headless);
 
-          StructureImportSettings.setTemperatureFactorType(tempfacType);
-
           af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
                   format);
 
@@ -399,8 +362,8 @@ public class Commands
         for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
         {
           String val = av.getValue();
-          SubVals subId = av.getSubVals();
-          SequenceI seq = getSpecifiedSequence(af, subId);
+          SubVals subVals = av.getSubVals();
+          SequenceI seq = getSpecifiedSequence(af, subVals);
           if (seq == null)
           {
             // Could not find sequence from subId, let's assume the first
@@ -418,10 +381,10 @@ public class Commands
             continue;
           }
           File structureFile = null;
-          if (subId.getContent() != null
-                  && subId.getContent().length() != 0)
+          if (subVals.getContent() != null
+                  && subVals.getContent().length() != 0)
           {
-            structureFile = new File(subId.getContent());
+            structureFile = new File(subVals.getContent());
             Console.debug("Using structure file (from argument) '"
                     + structureFile.getAbsolutePath() + "'");
           }
@@ -473,102 +436,71 @@ public class Commands
                     StructureViewer.ViewerType.JMOL.toString());
           }
 
-          // get tft, paeFilename, label?
-          /*
-           * ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
-           * Arg.TEMPFAC);
-           */
-          StructureChooser.openStructureFileForSequence(null, null, ap, seq,
-                  false, structureFile.getAbsolutePath(), null, null); // tft,
-          // paeFilename);
-        }
-      }
-    }
+          String structureFilepath = structureFile.getAbsolutePath();
 
-    // load a PAE file if given
-    if (avm.containsArg(Arg.PAEMATRIX))
-    {
-      AlignFrame af = afMap.get(id);
-      if (af != null)
-      {
-        for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
-        {
-          String val = av.getValue();
-          SubVals subVals = av.getSubVals();
-          String paeLabel = subVals.get("label");
-          File paeFile = new File(subVals.getContent());
-          String paePath = null;
-          try
+          // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
+          String paeFilepath = subVals.getWithSubstitutions(argParser, id,
+                  "paematrix");
+          String paeLabel = subVals.get("paelabel");
+          ArgValue paeAv = getArgAssociatedWithStructure(Arg.PAEMATRIX, avm,
+                  af, structureFilepath);
+          if (paeFilepath == null && paeAv != null)
           {
-            paePath = paeFile.getCanonicalPath();
-          } catch (IOException e)
+            SubVals sv = paeAv.getSubVals();
+            File paeFile = new File(sv.getContent());
+
+            paeLabel = sv.get("label");
+            try
+            {
+              paeFilepath = paeFile.getCanonicalPath();
+            } catch (IOException e)
+            {
+              paeFilepath = paeFile.getAbsolutePath();
+              Console.warn("Problem with the PAE file path: '"
+                      + paeFile.getPath() + "'");
+            }
+          }
+
+          // get TEMPFAC type from subvals or Arg.TEMPFAC
+          String tftString = subVals.get("tempfac");
+          TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null
+                  : TFType.DEFAULT;
+          ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
+                  af, structureFilepath);
+          if (tftString == null && tftAv != null)
           {
-            paePath = paeFile.getAbsolutePath();
-            Console.warn(
-                    "Problem with the PAE file path: '" + paePath + "'");
+            tftString = tftAv.getSubVals().getContent();
           }
-          String structid = subVals.get("structid");
-          String structfile = subVals.get("structfile");
-          String seqid = subVals.get("seqid");
-          int seqindex = subVals.getIndex();
-
-          // let's find a structure
-          if (structfile == null && structid == null && seqid == null
-                  && seqindex == SubVals.NOTSET)
+          if (tftString != null)
           {
-            ArgValue likelyStructure = avm
-                    .getClosestPreviousArgValueOfArg(av, Arg.STRUCTURE);
-            if (likelyStructure != null)
+            // get kind of temperature factor annotation
+            try
             {
-              SubVals sv = likelyStructure.getSubVals();
-              if (sv != null && sv.has(ArgValues.ID))
-              {
-                structid = sv.get(ArgValues.ID);
-              }
-              else
+              tft = TFType.valueOf(tftString.toUpperCase(Locale.ROOT));
+              Console.debug("Obtained Temperature Factor type of '" + tft
+                      + "' for structure '" + structureFilepath + "'");
+            } catch (IllegalArgumentException e)
+            {
+              // Just an error message!
+              StringBuilder sb = new StringBuilder().append("Cannot set ")
+                      .append(Arg.TEMPFAC.argString()).append(" to '")
+                      .append(tft)
+                      .append("', ignoring.  Valid values are: ");
+              Iterator<TFType> it = Arrays.stream(TFType.values())
+                      .iterator();
+              while (it.hasNext())
               {
-                structfile = likelyStructure.getValue();
-                Console.debug(
-                        "##### Using closest previous structure argument '"
-                                + structfile + "'");
+                sb.append(it.next().toString().toLowerCase(Locale.ROOT));
+                if (it.hasNext())
+                  sb.append(", ");
               }
+              Console.warn(sb.toString());
             }
           }
 
-          if (structfile != null)
-          {
-            Console.debug("##### Attaching paeFile '" + paePath + "' to "
-                    + "structfile=" + structfile);
-            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
-                    paeFile, seqindex, structfile, true, false, paeLabel);
-          }
-          else if (structid != null)
-          {
-            Console.debug("##### Attaching paeFile '" + paePath + "' to "
-                    + "structid=" + structid);
-            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
-                    paeFile, seqindex, structid, true, true, paeLabel);
-          }
-          else if (seqid != null)
-          {
-            Console.debug("##### Attaching paeFile '" + paePath + "' to "
-                    + "seqid=" + seqid);
-            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
-                    paeFile, seqindex, seqid, false, false, paeLabel);
-          }
-          else if (seqindex >= 0)
-          {
-            Console.debug("##### Attaching paeFile '" + paePath
-                    + "' to sequence index " + seqindex);
-            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
-                    paeFile, seqindex, null, false, false, paeLabel);
-          }
-          for (AlignmentViewPanel ap : af.getAlignPanels())
-          {
-            // required to readjust the height and position of the PAE
-            // annotation
-            ap.adjustAnnotationHeight();
-          }
+          // TODO pass PAE label
+          StructureChooser.openStructureFileForSequence(null, null, ap, seq,
+                  false, structureFilepath, tft, paeFilepath);
         }
       }
     }
@@ -670,4 +602,57 @@ public class Commands
     }
     return null;
   }
+
+  // returns the first Arg value intended for the structure structFilename
+  // (in the given AlignFrame from the ArgValuesMap)
+  private ArgValue getArgAssociatedWithStructure(Arg arg, ArgValuesMap avm,
+          AlignFrame af, String structFilename)
+  {
+    if (af != null)
+    {
+      for (ArgValue av : avm.getArgValueList(arg))
+      {
+        SubVals subVals = av.getSubVals();
+        String structid = subVals.get("structid");
+        String structfile = subVals.get("structfile");
+
+        // let's find a structure
+        if (structfile == null && structid == null)
+        {
+          ArgValue likelyStructure = avm.getClosestPreviousArgValueOfArg(av,
+                  Arg.STRUCTURE);
+          if (likelyStructure != null)
+          {
+            SubVals sv = likelyStructure.getSubVals();
+            if (sv != null && sv.has(ArgValues.ID))
+            {
+              structid = sv.get(ArgValues.ID);
+            }
+            else
+            {
+              structfile = likelyStructure.getValue();
+              Console.debug(
+                      "##### Comparing closest previous structure argument '"
+                              + structfile + "'");
+            }
+          }
+        }
+
+        if (structfile == null && structid != null)
+        {
+          StructureSelectionManager ssm = StructureSelectionManager
+                  .getStructureSelectionManager(Desktop.instance);
+          if (ssm != null)
+          {
+            structfile = ssm.findFileForPDBId(structid);
+          }
+        }
+        if (structfile != null && structfile.equals(structFilename))
+        {
+          return av;
+        }
+      }
+    }
+    return null;
+  }
 }

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 5f0cad6..0ff1845 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -480,9 +480,9 @@ public class ArgParser
     }
   }
 
-  private String makeSubstitutions(String val, String linkedId)
+  public String makeSubstitutions(String val, String linkedId)
   {
-    if (!this.substitutions)
+    if (!this.substitutions || val == null)
       return val;
 
     String subvals;

diff --git a/src/jalview/bin/argparser/SubVals.java b/src/jalview/bin/argparser/SubVals.java
index 6708cf9..196cd24 100644 (file)
--- a/src/jalview/bin/argparser/SubVals.java
+++ b/src/jalview/bin/argparser/SubVals.java
@@ -104,6 +104,11 @@ public class SubVals
     return index == NOTSET && (subValMap == null || subValMap.size() == 0);
   }
 
+  public String getWithSubstitutions(ArgParser ap, String id, String key)
+  {
+    return ap.makeSubstitutions(subValMap.get(key), id);
+  }
+
   public String get(String key)
   {
     return subValMap.get(key);

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 3fce931..fc73c27 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -28,9 +28,11 @@ import java.io.File;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
+import java.util.LinkedHashMap;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Locale;
+import java.util.Map;
 import java.util.concurrent.Callable;
 import java.util.concurrent.Executors;
 
@@ -45,11 +47,16 @@ import javax.swing.table.AbstractTableModel;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.fts.api.FTSData;
@@ -1711,10 +1718,21 @@ public class StructureChooser extends GStructureChooser
           AlignmentPanel ap, SequenceI seq, boolean prompt,
           String sFilename, TFType tft, String paeFilename)
   {
-    boolean headless = false;
+    openStructureFileForSequence(ssm, sc, ap, seq, prompt, sFilename, tft,
+            paeFilename, false, true);
+  }
+
+  public static void openStructureFileForSequence(
+          StructureSelectionManager ssm, StructureChooser sc,
+          AlignmentPanel ap, SequenceI seq, boolean prompt,
+          String sFilename, TFType tft, String paeFilename,
+          boolean forceHeadless, boolean showAnnotations)
+  {
+    boolean headless = forceHeadless;
     if (sc == null)
     {
       headless = true;
+      prompt = false;
       sc = new StructureChooser(new SequenceI[] { seq }, seq, ap, false);
     }
     if (ssm == null)
@@ -1724,11 +1742,38 @@ public class StructureChooser extends GStructureChooser
             sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
             tft, paeFilename);
 
-    StructureViewer sViewer = sc.launchStructureViewer(ssm,
-            new PDBEntry[]
-            { fileEntry }, ap, new SequenceI[] { seq });
+    // if headless, "false" in the sc constructor above will avoid GUI behaviour
+    // in sc.launchStructureViewer()
+    sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+            new SequenceI[]
+            { seq });
 
     if (headless)
       sc.mainFrame.dispose();
+
+    if (showAnnotations)
+      showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+  }
+
+  public static void showReferenceAnnotationsForSequence(AlignFrame af,
+          SequenceI sequence)
+  {
+    AlignViewport av = af.getCurrentView();
+    AlignmentI al = av.getAlignment();
+
+    List<SequenceI> forSequences = new ArrayList<>();
+    forSequences.add(sequence);
+    final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+    AlignmentUtils.findAddableReferenceAnnotations(forSequences, null,
+            candidates, al);
+    final SequenceGroup selectionGroup = av.getSelectionGroup();
+    AlignmentUtils.addReferenceAnnotations(candidates, al, selectionGroup);
+    for (AlignmentViewPanel ap : af.getAlignPanels())
+    {
+      // required to readjust the height and position of the PAE
+      // annotation
+      ap.adjustAnnotationHeight();
+    }
+
   }
 }

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index d0538c1..8044717 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -314,6 +314,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
 
     if (isStruct)
     {
+      // ###### WRITE A TEST for this bit of the logic addAlphaFoldPAE with
+      // different params.
       StructureSelectionManager ssm = StructureSelectionManager
               .getStructureSelectionManager(Desktop.instance);
       if (ssm != null)
@@ -474,6 +476,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     return paeDict;
   }
 
+  // ###### TEST THIS
   public static boolean importPaeJSONAsContactMatrixToStructure(
           StructureMapping[] smArray, InputStream paeInput, String label)
           throws IOException, ParseException
@@ -505,9 +508,9 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
             (Map<String, Object>) pae_obj);
     ((PAEContactMatrix) matrix).makeGroups(5f, true);
     AlignmentAnnotation cmannot = seq.addContactList(matrix);
-    seq.addAlignmentAnnotation(cmannot);
-    // seq.addAlignmentAnnotation(cmannot);
-
+    /* this already happens in Sequence.addContactList()
+     seq.addAlignmentAnnotation(cmannot);
+     */
     return true;
   }