JAL-629 implementation of --tempfac options

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

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 420e1d1..4ff82aa 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -1,13 +1,19 @@
 package jalview.bin;
 
 import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.bin.ArgParser.Arg;
 import jalview.bin.ArgParser.ArgValues;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.io.AppletFormatAdapter;
@@ -19,6 +25,7 @@ import jalview.io.IdentifyFile;
 import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.ws.dbsources.EBIAlfaFold;
 
 public class Commands
 {
@@ -67,7 +74,6 @@ public class Commands
   protected void processLinked(String id)
   {
     Map<Arg, ArgValues> m = argParser.linkedArgs(id);
-    FileLoader fileLoader = new FileLoader(!headless);
 
     /*
     // script to execute after all loading is completed one way or another
@@ -90,7 +96,6 @@ public class Commands
       {
         if (openFile == null)
           continue OPEN;
-        Console.debug("********** id = " + id + ", openFile = " + openFile);
 
         if (first)
         {
@@ -136,12 +141,55 @@ public class Commands
         af = afMap.get(id);
         if (af == null)
         {
+          // 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)
+          {
+            try
+            {
+              tempfacType = AlignmentAnnotation.TFType
+                      .valueOf(m.get(Arg.TEMPFAC).getValue()
+                              .toUpperCase(Locale.ROOT));
+              Console.debug("Obtained Temperature Factor type of '"
+                      + tempfacType + "'");
+            } catch (IllegalArgumentException e)
+            {
+              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();
+              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");
-          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
-                  format);
+          FileLoader fileLoader = new FileLoader(!headless);
+          af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format,
+                  tempfacType);
+
+          // wrap alignment?
+          if (m.get(Arg.WRAP) != null && m.get(Arg.WRAP).getBoolean())
+          {
+            af.getCurrentView().setWrapAlignment(true);
+          }
+
+          // change alignment frame title
           if (m.get(Arg.TITLE) != null)
             af.setTitle(m.get(Arg.TITLE).getValue());
+
+          // show secondary structure annotations?
           if (m.get(Arg.SSANNOTATION) != null
                   && !m.get(Arg.SSANNOTATION).getBoolean())
           {
@@ -151,19 +199,47 @@ public class Commands
                     Collections.singleton("Secondary Structure"), null,
                     false, false);
           }
+
+          // show temperature factor annotations?
           if (m.get(Arg.NOTEMPFAC) != null
                   && m.get(Arg.NOTEMPFAC).getBoolean())
           {
             // do this better (annotation types?)
+            List<String> hideThese = new ArrayList<>();
+            hideThese.add("Temperature Factor");
+            hideThese.add(MessageManager
+                    .getString("label.alphafold_reliability"));
             AlignmentUtils.showOrHideSequenceAnnotations(
-                    af.getCurrentView().getAlignment(),
-                    Collections.singleton("Temperature Factor"), null,
-                    false, false);
-            AlignmentUtils.showOrHideSequenceAnnotations(
-                    af.getCurrentView().getAlignment(),
-                    Collections.singleton("Alphafold Reliability"), null,
+                    af.getCurrentView().getAlignment(), hideThese, null,
                     false, false);
           }
+          else
+          {
+            if (m.get(Arg.TEMPFAC_LABEL) != null)
+            {
+              AlignmentAnnotation aa = AlignmentUtils
+                      .getFirstSequenceAnnotationOfType(
+                              af.getCurrentView().getAlignment(),
+                              AlignmentAnnotation.LINE_GRAPH);
+              Console.debug("***** Trying to change label from '"
+                      + (aa == null ? aa : aa.label) + "' to '"
+                      + m.get(Arg.TEMPFAC_LABEL).getValue() + "'");
+              if (aa != null)
+              {
+                aa.label = m.get(Arg.TEMPFAC_LABEL).getValue();
+              }
+            }
+          }
+
+          //
+
+          // load a pAE file?
+          if (m.get(Arg.PAEMATRIX) != null)
+          {
+            File paeFile = new File(m.get(Arg.PAEMATRIX).getValue());
+            EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+                    paeFile);
+          }
 
           // store the AlignFrame for this id
           afMap.put(id, af);