X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=2d7f02b8fad8516c14f698ad92a4be92d2b0da08;hb=453fa24ab502aaca4ffccf3590f97c897b9580b3;hp=1f904cdfed5ddf1ca497fb7c4d61236b69b98b20;hpb=b64d494eebb7f9cf14c61e50568f41887fca5c26;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 1f904cd..2d7f02b 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -14,9 +14,11 @@ import jalview.analysis.AlignmentUtils;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.ArgParser.Arg;
 import jalview.bin.ArgParser.ArgValues;
-import jalview.bin.ArgParser.SubId;
+import jalview.bin.ArgParser.SubVal;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
@@ -26,11 +28,17 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
 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
 {
@@ -42,14 +50,21 @@ public class Commands
 
   private Map<String, AlignFrame> afMap;
 
-  public static void processArgs(ArgParser ap, boolean h)
+  public static boolean processArgs(ArgParser ap, boolean h)
   {
     argParser = ap;
     headless = h;
+    boolean argsWereParsed = false;
+    if (headless)
+    {
+      System.setProperty("java.awt.headless", "true");
+    }
+
     if (argParser != null && argParser.linkedIds() != null)
     {
       for (String id : argParser.linkedIds())
       {
+        Console.debug("##### id=" + id);
         Commands cmds = new Commands();
         if (id == null)
         {
@@ -59,8 +74,25 @@ public class Commands
         {
           cmds.processLinked(id);
         }
+        cmds.processImages(id);
+        argsWereParsed |= cmds.wereParsed();
       }
+
     }
+    if (argParser.getBool(Arg.QUIT))
+    {
+      Jalview.getInstance().quit();
+      return true;
+    }
+    // carry on with jalview.bin.Jalview
+    return argsWereParsed;
+  }
+
+  boolean argsWereParsed = false;
+
+  private boolean wereParsed()
+  {
+    return argsWereParsed;
   }
 
   public Commands()
@@ -76,6 +108,8 @@ public class Commands
 
   protected void processUnlinked(String id)
   {
+    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+
     processLinked(id);
   }
 
@@ -93,18 +127,18 @@ public class Commands
     FileFormatI format = null;
     DataSourceType protocol = null;
     */
-
-    if (m.get(Arg.OPEN) != null)
+    if (ArgParser.getArgValues(m, Arg.OPEN) != null)
     {
       long progress = -1;
 
       boolean first = true;
       AlignFrame af;
-      OPEN: for (String openFile : m.get(Arg.OPEN).getValues())
+      for (String openFile : ArgParser.getValues(m, Arg.OPEN))
       {
         if (openFile == null)
-          continue OPEN;
+          continue;
 
+        argsWereParsed = true;
         if (first)
         {
           first = false;
@@ -129,7 +163,6 @@ public class Commands
             if (!(new File(openFile)).exists())
             {
               Console.warn("Can't find file '" + openFile + "'");
-              continue OPEN;
             }
           }
         }
@@ -180,26 +213,25 @@ public class Commands
            */
 
           // get kind of temperature factor annotation
-          AlignmentAnnotation.TFType tempfacType = null;
-          if ((m.get(Arg.NOTEMPFAC) == null
-                  || !m.get(Arg.NOTEMPFAC).getBoolean())
-                  && m.get(Arg.TEMPFAC) != null)
+          StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
+          if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
+                  && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
           {
             try
             {
-              tempfacType = AlignmentAnnotation.TFType
-                      .valueOf(m.get(Arg.TEMPFAC).getValue()
-                              .toUpperCase(Locale.ROOT));
+              tempfacType = StructureImportSettings.TFType.valueOf(ArgParser
+                      .getValue(m, Arg.TEMPFAC).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.getName()).append(" to '")
                       .append(tempfacType)
                       .append("', ignoring.  Valid values are: ");
-              Iterator<AlignmentAnnotation.TFType> it = Arrays
-                      .stream(AlignmentAnnotation.TFType.values())
+              Iterator<StructureImportSettings.TFType> it = Arrays
+                      .stream(StructureImportSettings.TFType.values())
                       .iterator();
               while (it.hasNext())
               {
@@ -214,24 +246,26 @@ public class Commands
           Console.debug(
                   "Opening '" + openFile + "' in new alignment frame");
           FileLoader fileLoader = new FileLoader(!headless);
-          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format,
-                  tempfacType);
+
+          StructureImportSettings.setTemperatureFactorType(tempfacType);
+
+          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+                  format);
 
           // wrap alignment?
-          if (m.get(Arg.WRAP) != null && m.get(Arg.WRAP).getBoolean())
+          if (ArgParser.getBoolean(m, Arg.WRAP))
           {
             af.getCurrentView().setWrapAlignment(true);
           }
 
           // change alignment frame title
-          if (m.get(Arg.TITLE) != null)
-            af.setTitle(m.get(Arg.TITLE).getValue());
+          if (ArgParser.getValue(m, Arg.TITLE) != null)
+            af.setTitle(ArgParser.getValue(m, Arg.TITLE));
 
           /* hacky approach to hiding the annotations */
           // show secondary structure annotations?
-          if (m.get(Arg.SSANNOTATION) != null)
+          if (ArgParser.getBoolean(m, Arg.SSANNOTATION))
           {
-            boolean showSS = m.get(Arg.SSANNOTATION).getBoolean();
             // do this better (annotation types?)
             AlignmentUtils.showOrHideSequenceAnnotations(
                     af.getCurrentView().getAlignment(),
@@ -240,14 +274,12 @@ public class Commands
           }
 
           // show temperature factor annotations?
-          if (m.get(Arg.NOTEMPFAC) != null
-                  && m.get(Arg.NOTEMPFAC).getBoolean())
+          if (ArgParser.getBoolean(m, Arg.NOTEMPFAC))
           {
             // do this better (annotation types?)
             List<String> hideThese = new ArrayList<>();
             hideThese.add("Temperature Factor");
-            hideThese.add(MessageManager
-                    .getString("label.alphafold_reliability"));
+            hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
             AlignmentUtils.showOrHideSequenceAnnotations(
                     af.getCurrentView().getAlignment(), hideThese, null,
                     false, false);
@@ -257,13 +289,13 @@ public class Commands
            if (showTemperatureFactor)
              */
           {
-            if (m.get(Arg.TEMPFAC_LABEL) != null)
+            if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null)
             {
               AlignmentAnnotation aa = AlignmentUtils
                       .getFirstSequenceAnnotationOfType(
                               af.getCurrentView().getAlignment(),
                               AlignmentAnnotation.LINE_GRAPH);
-              String label = m.get(Arg.TEMPFAC_LABEL).getValue();
+              String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL);
               if (aa != null)
               {
                 aa.label = label;
@@ -279,6 +311,16 @@ public class Commands
 
           // store the AlignFrame for this id
           afMap.put(id, af);
+
+          // is it its own structure file?
+          if (format.isStructureFile())
+          {
+            StructureSelectionManager ssm = StructureSelectionManager
+                    .getStructureSelectionManager(Desktop.instance);
+            SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
+            ssm.computeMapping(false, new SequenceI[] { seq }, null,
+                    openFile, DataSourceType.FILE, null);
+          }
         }
         else
         {
@@ -298,31 +340,55 @@ public class Commands
           Console.error("Could not open any files in headless mode");
           System.exit(1);
         }
-      }
-      else
-      {
-        Console.warn("No more files to open");
-        if (desktop != null)
-          desktop.setProgressBar(null, progress);
+        else
+        {
+          Console.warn("No more files to open");
+          if (desktop != null)
+            desktop.setProgressBar(null, progress);
+        }
       }
 
     }
 
     // load a pAE file if given
-    if (m.get(Arg.PAEMATRIX) != null)
+    if (ArgParser.getValues(m, Arg.PAEMATRIX) != null)
     {
       AlignFrame af = afMap.get(id);
       if (af != null)
       {
-        for (String val : m.get(Arg.PAEMATRIX).getValues())
+        for (String val : ArgParser.getValues(m, Arg.PAEMATRIX))
         {
-          SubId subId = ArgParser.getSubId(val);
-          File paeFile = new File(subId.content);
-          EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
-                  paeFile, subId.index,
-                  "id".equals(subId.keyName) ? subId.keyValue : null);
-          // required to readjust the height and position of the pAE
-          // annotation
+          SubVal subVal = ArgParser.getSubVal(val);
+          File paeFile = new File(subVal.content);
+          String structId = "structid".equals(subVal.keyName)
+                  ? subVal.keyValue
+                  : null;
+          if (subVal.notSet())
+          {
+            // take structid from pdbfilename
+          }
+          if ("structfile".equals(subVal.keyName))
+          {
+            EBIAlfaFold.addAlphaFoldPAEToStructure(
+                    af.getCurrentView().getAlignment(), paeFile,
+                    subVal.index, subVal.keyValue, false);
+          }
+          else if ("structid".equals(subVal.keyName))
+          {
+            EBIAlfaFold.addAlphaFoldPAEToStructure(
+                    af.getCurrentView().getAlignment(), paeFile,
+                    subVal.index, subVal.keyValue, true);
+          }
+          else
+          {
+            EBIAlfaFold.addAlphaFoldPAEToSequence(
+                    af.getCurrentView().getAlignment(), paeFile,
+                    subVal.index,
+                    "seqid".equals(subVal.keyName) ? subVal.keyValue
+                            : null);
+            // required to readjust the height and position of the pAE
+            // annotation
+          }
           for (AlignmentViewPanel ap : af.getAlignPanels())
           {
             ap.adjustAnnotationHeight();
@@ -332,21 +398,22 @@ public class Commands
     }
 
     // open the structure (from same PDB file or given PDBfile)
-    if (m.get(Arg.NOSTRUCTURE) == null
-            || !m.get(Arg.NOQUESTIONNAIRE).getBoolean())
+    if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
     {
       AlignFrame af = afMap.get(id);
-      if (m.get(Arg.STRUCTURE) != null)
+      if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
       {
-        STRUCTURE: for (String val : m.get(Arg.STRUCTURE).getValues())
+        for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
         {
-          SubId subId = new SubId(val);
+          SubVal subId = new SubVal(val);
           SequenceI seq = getSpecifiedSequence(af, subId);
           if (seq == null)
           {
             Console.warn("Could not find sequence for argument --"
                     + Arg.STRUCTURE + "=" + val);
-            break STRUCTURE;
+            // you probably want to continue here, not break
+            // break;
+            continue;
           }
           File structureFile = null;
           if (subId.content != null && subId.content.length() != 0)
@@ -368,14 +435,14 @@ public class Commands
           if (structureFile == null)
           {
             Console.warn("Not provided structure file with '" + val + "'");
-            continue STRUCTURE;
+            continue;
           }
 
           if (!structureFile.exists())
           {
             Console.warn("Structure file '"
                     + structureFile.getAbsoluteFile() + "' not found.");
-            continue STRUCTURE;
+            continue;
           }
 
           Console.debug("Using structure file "
@@ -388,28 +455,94 @@ public class Commands
         }
       }
     }
+
+    boolean doShading = ArgParser.getBoolean(m, Arg.TEMPFAC_SHADING);
+    if (doShading)
+    {
+      AlignFrame af = afMap.get(id);
+      for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+              .findAnnotation(PDBChain.class.getName().toString()))
+      {
+        AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+                af.alignPanel.av.getGlobalColourScheme(), 0);
+        acg.setSeqAssociated(true);
+        af.changeColour(acg);
+        Console.info("Changed colour " + acg.toString());
+      }
+    }
   }
 
-  private SequenceI getSpecifiedSequence(AlignFrame af, SubId subId)
+  protected void processImages(String id)
   {
-    SequenceI seq = null;
-    SequenceI[] sequences = af.getCurrentView().getAlignment()
-            .getSequencesArray();
-    if (-1 < subId.index && subId.index < sequences.length)
+    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+    AlignFrame af = afMap.get(id);
+
+    if (af == null)
     {
-      seq = sequences[subId.index];
+      Console.warn("Did not have an alignment window for id=" + id);
+      return;
     }
-    else if ("id".equals(subId.keyName))
+
+    if (ArgParser.getValues(m, Arg.IMAGE) != null)
     {
-      for (SequenceI s : sequences)
+      for (String val : ArgParser.getValues(m, Arg.IMAGE))
       {
-        if (s.getDisplayId(false).equals(subId.keyValue))
+        SubVal subVal = new SubVal(val);
+        String type = "png"; // default
+        String fileName = subVal.content;
+        File file = new File(fileName);
+        if ("type".equals(subVal.keyName))
+        {
+          type = subVal.keyValue;
+        }
+        else if (fileName != null)
         {
-          seq = s;
+          for (String ext : new String[] { "svg", "png", "html" })
+          {
+            if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+            {
+              type = ext;
+            }
+          }
+        }
+        // for moment we disable JSON export
+        Cache.setPropsAreReadOnly(true);
+        Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
+        switch (type)
+        {
+        case "svg":
+          Console.debug("Outputting type '" + type + "' to " + fileName);
+          af.createSVG(file);
+          break;
+        case "png":
+          Console.debug("Outputting type '" + type + "' to " + fileName);
+          af.createPNG(file);
+          break;
+        case "html":
+          Console.debug("Outputting type '" + type + "' to " + fileName);
+          HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+          htmlSVG.exportHTML(fileName);
+          break;
+        default:
+          Console.warn("--image type '" + type + "' not known. Ignoring");
           break;
         }
       }
     }
-    return seq;
+  }
+
+  private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId)
+  {
+    AlignmentI al = af.getCurrentView().getAlignment();
+    if (-1 < subId.index && subId.index < al.getSequences().size())
+    {
+      return al.getSequenceAt(subId.index);
+    }
+    else if ("id".equals(subId.keyName))
+    {
+      return al.findName(subId.keyValue);
+    }
+    return null;
   }
 }