JAL-629 Test and fix --annotation --ssannotation args. Added a viewerType arg/subval...

[jalview.git] / src / jalview / bin / Commands.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 6d514b0..fc2ee1a 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -5,7 +5,7 @@ import java.io.IOException;
 import java.util.AbstractMap;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collections;
+import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
@@ -16,11 +16,11 @@ import java.util.Map.Entry;
 import jalview.analysis.AlignmentUtils;
 import jalview.bin.argparser.Arg;
 import jalview.bin.argparser.ArgParser;
+import jalview.bin.argparser.ArgParser.Position;
 import jalview.bin.argparser.ArgValue;
 import jalview.bin.argparser.ArgValues;
 import jalview.bin.argparser.ArgValuesMap;
 import jalview.bin.argparser.SubVals;
-import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
@@ -30,6 +30,7 @@ import jalview.gui.Desktop;
 import jalview.gui.Preferences;
 import jalview.gui.StructureChooser;
 import jalview.gui.StructureViewer;
+import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -38,13 +39,11 @@ import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
-import jalview.schemes.AnnotationColourGradient;
 import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import mc_view.PDBChain;
 
 public class Commands
 {
@@ -226,11 +225,11 @@ public class Commands
         {
           /*
            * this approach isn't working yet // get default annotations before opening
-           * AlignFrame if (m.get(Arg.SSANNOTATION) != null) {
-           * Console.debug("##### SSANNOTATION=" + m.get(Arg.SSANNOTATION).getBoolean());
+           * AlignFrame if (m.get(Arg.SSANNOTATIONS) != null) {
+           * Console.debug("##### SSANNOTATIONS=" + m.get(Arg.SSANNOTATIONS).getBoolean());
            * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" +
            * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure =
-           * (m.get(Arg.SSANNOTATION) != null) ? m.get(Arg.SSANNOTATION).getBoolean() :
+           * (m.get(Arg.SSANNOTATIONS) != null) ? m.get(Arg.SSANNOTATIONS).getBoolean() :
            * false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ?
            * !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" +
            * showTemperatureFactor + ", showSS=" + showSecondaryStructure);
@@ -246,6 +245,10 @@ public class Commands
 
           af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
                   format);
+          boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+                  Arg.ANNOTATIONS, av.getSubVals(), null,
+                  "SHOW_ANNOTATIONS", true);
+          af.setAnnotationsVisibility(showAnnotations, false, true);
 
           // wrap alignment?
           if (avm.getBoolean(Arg.WRAP))
@@ -263,15 +266,19 @@ public class Commands
           if (avm.containsArg(Arg.TITLE))
             af.setTitle(avm.getValue(Arg.TITLE));
 
-          /* hacky approach to hiding the annotations */
           // show secondary structure annotations?
-          if (avm.getBoolean(Arg.SSANNOTATION))
+          boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+                  Arg.SSANNOTATIONS, av.getSubVals(), null,
+                  "STRUCT_FROM_PDB", true);
+          if (avm.getBoolean(Arg.SSANNOTATIONS))
           {
-            // do this better (annotation types?)
+            af.setAnnotationsVisibility(showSSAnnotations, true, false);
+            /*
             AlignmentUtils.showOrHideSequenceAnnotations(
                     af.getCurrentView().getAlignment(),
                     Collections.singleton("Secondary Structure"), null,
                     false, false);
+             */
           }
 
           // show temperature factor annotations?
@@ -291,6 +298,7 @@ public class Commands
            * (showTemperatureFactor)
            */
           {
+            /*
             if (avm.containsArg(Arg.TEMPFAC_LABEL))
             {
               AlignmentAnnotation aa = AlignmentUtils
@@ -309,6 +317,7 @@ public class Commands
                                 + label);
               }
             }
+            */
           }
 
           // store the AlignFrame for this id
@@ -463,7 +472,13 @@ public class Commands
             }
           }
 
-          // get TEMPFAC type from subvals or Arg.TEMPFAC
+          // showing annotations from structure file or not
+          boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
+                  Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+                  true);
+
+          // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
+          // reference annotations
           String tftString = subVals.get("tempfac");
           TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null
                   : TFType.DEFAULT;
@@ -500,13 +515,36 @@ public class Commands
             }
           }
 
-          // TODO pass PAE label
+          String sViewer = ArgParser.getFromSubValArgOrPref(avm,
+                  Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals,
+                  "viewer", null, "jmol");
+          ViewerType viewerType = null;
+          if (!"none".equals(sViewer))
+          {
+            for (ViewerType v : EnumSet.allOf(ViewerType.class))
+            {
+              String name = v.name().toLowerCase(Locale.ROOT)
+                      .replaceAll(" ", "");
+              if (sViewer.equals(name))
+              {
+                viewerType = v;
+                break;
+              }
+            }
+          }
+
+          boolean addTempFac = tft != null
+                  || Cache.getDefault("ADD_TEMPFACT_ANN", false);
+
+          // TODO use ssFromStructure
           StructureChooser.openStructureFileForSequence(null, null, ap, seq,
-                  false, structureFilepath, tft, paeFilepath, false);
+                  false, structureFilepath, tft, paeFilepath, false,
+                  ssFromStructure, false, viewerType);
         }
       }
     }
 
+    /*
     boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
     if (doShading)
     {
@@ -521,6 +559,7 @@ public class Commands
         Console.info("Changed colour " + acg.toString());
       }
     }
+    */
 
     return theseArgsWereParsed;
   }