Merge pull request #868 from bbreton/issue-836-sequence-track-saving-…

…and-commands Git Issue #836 SequenceTrack commands, preferences and session work
igvteam · Dec 4, 2020 · 5c8a057 · 5c8a057
2 parents 83d987d + fe1b110
commit 5c8a057
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Showing 8 changed files with 93 additions and 1 deletion.
diff --git a/src/main/java/org/broad/igv/batch/CommandExecutor.java b/src/main/java/org/broad/igv/batch/CommandExecutor.java
@@ -36,6 +36,7 @@
 import org.broad.igv.feature.Locus;
 import org.broad.igv.feature.Range;
 import org.broad.igv.feature.RegionOfInterest;
+import org.broad.igv.feature.Strand;
 import org.broad.igv.feature.genome.GenomeManager;
 import org.broad.igv.google.Ga4ghAPIHelper;
 import org.broad.igv.google.OAuthUtils;
@@ -45,6 +46,7 @@
 import org.broad.igv.sam.AlignmentTrack;
 import org.broad.igv.track.RegionScoreType;
 import org.broad.igv.track.Track;
+import org.broad.igv.track.SequenceTrack;
 import org.broad.igv.ui.IGV;
 import org.broad.igv.ui.panel.FrameManager;
 import org.broad.igv.ui.util.MessageUtils;
@@ -133,6 +135,20 @@ public String execute(String command) {
             } else if (cmd.equalsIgnoreCase("collapse")) {
                 String trackName = parseTrackName(param1);
                 igv.setTrackDisplayMode(Track.DisplayMode.COLLAPSED, trackName);
+            } else if (cmd.equalsIgnoreCase("setSequenceStrand")) {
+                igv.setSequenceTrackStrand(Strand.fromString(param1));
+            } else if (cmd.equalsIgnoreCase("setSequenceShowTranslation")) {
+                boolean showTranslation;
+                try {
+                    if (param1.equalsIgnoreCase("true") || param1.equalsIgnoreCase("false")) {
+                        showTranslation = Boolean.valueOf(param1);
+                    } else {
+                        return "ERROR: showTranslation value (" + param1 + ")is not 'true' or 'false'.";
+                    }
+                } catch (IllegalArgumentException e) {
+                    return e.getMessage();
+                }
+                igv.setSequenceShowTranslation(showTranslation);
             } else if (cmd.equalsIgnoreCase("expand")) {
                 String trackName = parseTrackName(param1);
                 igv.setTrackDisplayMode(Track.DisplayMode.EXPANDED, trackName);

diff --git a/src/main/java/org/broad/igv/feature/Strand.java b/src/main/java/org/broad/igv/feature/Strand.java
@@ -37,6 +37,8 @@ public enum Strand {
     NONE, POSITIVE, NEGATIVE;
 
     public static Strand fromString(String strandString) {
-        return strandString.equals("+") ? POSITIVE : (strandString.equals("-") ? NEGATIVE : NONE);
+        return strandString.equals("+") || strandString.equalsIgnoreCase("POSITIVE")
+                ? POSITIVE : (strandString.equals("-") || strandString.equalsIgnoreCase("NEGATIVE")
+                ? NEGATIVE : NONE);
     }
 }
diff --git a/src/main/java/org/broad/igv/prefs/Constants.java b/src/main/java/org/broad/igv/prefs/Constants.java
@@ -163,6 +163,7 @@ private Constants() {}  // Prevent instantiation
     public static final String KNOWN_SNPS = "KNOWN_SNPS_FILE";
 
     // Sequence track settings
+    public static final String SEQUENCE_TRANSLATION_STRAND = "SEQUENCE_TRANSLATION_STRAND";
     public static final String SHOW_SEQUENCE_TRANSLATION = "SHOW_SEQUENCE_TRANSLATION";
     public static final String MAX_SEQUENCE_RESOLUTION = "MAX_SEQUENCE_RESOLUTION";
     public static final String COLOR_A = "COLOR.A";

diff --git a/src/main/java/org/broad/igv/track/AbstractTrack.java b/src/main/java/org/broad/igv/track/AbstractTrack.java
@@ -32,6 +32,7 @@
 import org.broad.igv.Globals;
 import org.broad.igv.event.IGVEventBus;
 import org.broad.igv.event.IGVEventObserver;
+import org.broad.igv.feature.Strand;
 import org.broad.igv.prefs.Constants;
 import org.broad.igv.prefs.PreferencesManager;
 import org.broad.igv.renderer.*;
@@ -888,6 +889,10 @@ public void setDisplayMode(DisplayMode mode) {
         this.displayMode = mode;
     }
 
+    public void setSequenceTranslationStrandValue(Strand strand) {}
+
+    public void setShouldShowTranslationCommand(boolean shouldShowTranslation) {}
+
 
     public String getNameValueString(int y) {
 

diff --git a/src/main/java/org/broad/igv/track/SequenceTrack.java b/src/main/java/org/broad/igv/track/SequenceTrack.java
@@ -48,6 +48,8 @@
 import org.broad.igv.ui.panel.IGVPopupMenu;
 import org.broad.igv.ui.panel.ReferenceFrame;
 import org.broad.igv.ui.util.UIUtilities;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
 
 import javax.swing.*;
 import java.awt.*;
@@ -61,6 +63,7 @@
 
 import static org.broad.igv.prefs.Constants.MAX_SEQUENCE_RESOLUTION;
 import static org.broad.igv.prefs.Constants.SHOW_SEQUENCE_TRANSLATION;
+import static org.broad.igv.prefs.Constants.SEQUENCE_TRANSLATION_STRAND;
 
 
 /**
@@ -91,6 +94,7 @@ public SequenceTrack(String name) {
         super(null, name, name);
         setSortable(false);
         shouldShowTranslation = PreferencesManager.getPreferences().getAsBoolean(SHOW_SEQUENCE_TRANSLATION);
+        strand = Strand.fromString(PreferencesManager.getPreferences().get(SEQUENCE_TRANSLATION_STRAND));
         loadedIntervalCache = Collections.synchronizedMap(new HashMap<>());
         sequenceVisible = Collections.synchronizedMap(new HashMap<>());
         IGVEventBus.getInstance().subscribe(FrameManager.ChangeEvent.class, this);
@@ -314,12 +318,29 @@ private void flipStrand() {
 
     }
 
+    public void setSequenceTranslationStrandValue(Strand strandValue) {
+        strand = strandValue;
+        PreferencesManager.getPreferences().put(SEQUENCE_TRANSLATION_STRAND, strand.toString());
+        IGV.getInstance().clearSelections();
+        repaint();
+    }
+
     public void setShouldShowTranslation(boolean shouldShowTranslation) {
         this.shouldShowTranslation = shouldShowTranslation;
         // Remember this choice
         PreferencesManager.getPreferences().put(SHOW_SEQUENCE_TRANSLATION, shouldShowTranslation);
     }
 
+    public void setShouldShowTranslationCommand(boolean shouldShowTranslation) {
+        this.shouldShowTranslation = shouldShowTranslation;
+        setShouldShowTranslation(shouldShowTranslation);
+        repaint();
+        IGV.getInstance().repaint();
+        IGV.getInstance().clearSelections();
+        // Remember this choice
+        PreferencesManager.getPreferences().put(SHOW_SEQUENCE_TRANSLATION, shouldShowTranslation);
+    }
+
 
     /**
      * Override to return a specialized popup menu
@@ -445,4 +466,27 @@ public void refreshAminoAcids() {
             this.negAA = negAA;
         }
     }
+
+    public void marshalXML(Document document, Element element) {
+
+        super.marshalXML(document, element);
+
+        element.setAttribute("shouldShowTranslation", String.valueOf(shouldShowTranslation));
+        element.setAttribute("sequenceTranslationStrandValue", String.valueOf(strand));
+
+    }
+
+    @Override
+    public void unmarshalXML(Element element, Integer version) {
+
+        super.unmarshalXML(element, version);
+
+        if (element.hasAttribute("shouldShowTranslation")) {
+            this.shouldShowTranslation = Boolean.valueOf(element.getAttribute("shouldShowTranslation"));
+        }
+        if (element.hasAttribute("sequenceTranslationStrandValue")) {
+            this.strand = Strand.fromString(element.getAttribute("sequenceTranslationStrandValue"));
+        }
+    }
+
 }
diff --git a/src/main/java/org/broad/igv/track/Track.java b/src/main/java/org/broad/igv/track/Track.java
@@ -31,6 +31,7 @@
 
 
 import htsjdk.tribble.Feature;
+import org.broad.igv.feature.Strand;
 import org.broad.igv.renderer.ContinuousColorScale;
 import org.broad.igv.renderer.DataRange;
 import org.broad.igv.renderer.Renderer;
@@ -130,6 +131,9 @@ void renderAttributes(Graphics2D graphics, Rectangle trackRectangle, Rectangle v
 
     void setUrl(String url);
 
+    void setSequenceTranslationStrandValue(Strand strandValue);
+    void setShouldShowTranslationCommand(boolean shouldShowTranslation);
+
     ResourceLocator getResourceLocator();
 
     /**

diff --git a/src/main/java/org/broad/igv/ui/IGV.java b/src/main/java/org/broad/igv/ui/IGV.java
@@ -1617,6 +1617,25 @@ public void setTrackDisplayMode(Track.DisplayMode mode, String trackName) {
     }
 
 
+    public void setSequenceTrackStrand(Strand trackStrand) {
+        for (Track t : getAllTracks()) {
+            if (t.getName().equals("Reference sequence")) {
+                t.setSequenceTranslationStrandValue(trackStrand);
+            }
+        }
+
+    }
+
+    public void setSequenceShowTranslation(boolean shouldShowTranslation) {
+        for (Track t : getAllTracks()) {
+            if (t.getName().equals("Reference sequence")) {
+                t.setShouldShowTranslationCommand(shouldShowTranslation);
+            }
+        }
+
+    }
+
+
     /**
      * Reset the overlay tracks collection.  Currently the only overlayable track
      * type is Mutation.  This method finds all mutation tracks and builds a map

diff --git a/src/main/resources/org/broad/igv/prefs/preferences.tab b/src/main/resources/org/broad/igv/prefs/preferences.tab
@@ -247,6 +247,7 @@ DEFAULT_GENOME_KEY	hg19
 IGV.track.height	15
 FLANKING_REGION	2000
 SHOW_SEQUENCE_TRANSLATION	FALSE
+SEQUENCE_TRANSLATION_STRAND	POSITIVE
 AUTO_UPDATE_GENOMES	TRUE
 GWAS_TRACK_HEIGHT	200
 GWAS_DESCRIPTION_CACHE_SIZE	10000