JAL-4047 - proof of concept for JAL-4048 - display columns of info in sequence ID...

[jalview.git] / src / jalview / viewmodel / seqfeatures / IdColumns.java

diff --git a/src/jalview/viewmodel/seqfeatures/IdColumns.java b/src/jalview/viewmodel/seqfeatures/IdColumns.java
new file mode 100644 (file)
index 0000000..2f113f2
--- /dev/null
+++ b/src/jalview/viewmodel/seqfeatures/IdColumns.java
@@ -0,0 +1,204 @@
+package jalview.viewmodel.seqfeatures;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Vector;
+
+import jalview.api.DBRefEntryI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
+
+public class IdColumns
+{
+
+  AlignmentI alignment = null;
+
+  public IdColumns(AlignmentI al)
+  {
+    alignment = al;
+    columns.put(STRUCTURES_NUM.getLabel(), STRUCTURES_NUM);
+    updateTypeList();
+  }
+
+  public final static IdColumn STRUCTURES_NUM;
+  static
+  {
+    STRUCTURES_NUM = new IdColumn("3D Structures",
+            "Number of associated structure files", false);
+  }
+
+  LinkedHashMap<String, IdColumn> columns = new LinkedHashMap<String, IdColumn>();
+
+  /**
+   * register a feature on the columnset
+   * 
+   * @param sf
+   * @return true if feature was not seen before
+   */
+  boolean updateListForFeature(SequenceFeature sf)
+  {
+    String colname = sf.getType();
+    if (columns.get(colname) != null)
+    {
+      return false;
+    }
+
+    IdColumn col = new IdColumn(colname,
+            "Nonpositional feature: " + colname, false);
+    col.featureTypeName = sf.getType();
+    // col.featureGroupName = sf.getFeatureGroup();
+    columns.put(colname, col);
+    return true;
+  }
+
+  boolean updateListForDbxref(DBRefEntryI dbref)
+  {
+    String colname = dbref.getSource();
+    if (columns.get(colname) != null)
+    {
+      return false;
+    }
+
+    IdColumn col = new IdColumn(colname,
+            "Database CrossReference: " + colname, false);
+    col.DbRefName = colname;
+    // col.featureGroupName = sf.getFeatureGroup();
+    columns.put(colname, col);
+    return true;
+  }
+
+  public void updateTypeList()
+  {
+    for (SequenceI sq : alignment.getSequences())
+    {
+      SequenceI seq = sq;
+      while (seq.getDatasetSequence() != null)
+      {
+        seq = seq.getDatasetSequence();
+      }
+
+      SequenceFeaturesI sqf = seq.getFeatures();
+      List<SequenceFeature> nonpos = sqf.getNonPositionalFeatures();
+      if (nonpos != null)
+      {
+        for (SequenceFeature sf : nonpos)
+        {
+          updateListForFeature(sf);
+        }
+      }
+      for (DBRefEntryI dbr : seq.getDBRefs())
+      {
+        updateListForDbxref(dbr);
+      }
+    }
+  }
+
+  public void toggleVisible(String column)
+  {
+    IdColumn col = columns.get(column);
+    if (col != null)
+    {
+      col.visible = !col.visible;
+    }
+  }
+
+  public List<IdColumn> getVisible()
+  {
+    // probably want to cache this
+    ArrayList<IdColumn> vis = new ArrayList();
+    for (IdColumn col : columns.values())
+    {
+      if (col.visible)
+      {
+        vis.add(col);
+      }
+    }
+    return vis;
+  }
+
+  public final class ColumnCell
+  {
+    public final String label;
+
+    public final Color bg;
+
+    public final Color fg;
+
+    public ColumnCell(final String label, final Color bg, final Color fg)
+    {
+      this.label = label;
+      this.bg = bg;
+      this.fg = fg;
+    }
+  }
+
+  /**
+   * render the column value for this sequence
+   * 
+   * @param seq
+   * @param col
+   * @return
+   */
+  public ColumnCell getCellFor(SequenceI seq, IdColumn col)
+  {
+    ColumnCell cell = null;
+    if (col != null)
+    {
+      if (col == STRUCTURES_NUM)
+      {
+        while (seq.getDatasetSequence() != null)
+        {
+          seq = seq.getDatasetSequence();
+        }
+        Vector pdbE = seq.getAllPDBEntries();
+        if (pdbE == null)
+        {
+          return null;
+        }
+        return new ColumnCell("" + pdbE.size(), Color.red, Color.white);
+      }
+      if (col.featureTypeName != null)
+      {
+        List<SequenceFeature> np = seq.getFeatures()
+                .getNonPositionalFeatures(col.featureTypeName);
+        if (np != null)
+        {
+          for (SequenceFeature npfeat : np)
+          {
+            // nb deal with multiplicities!
+            if (col.featureGroupName != null && npfeat.featureGroup != null
+                    && npfeat.featureGroup.equals(col.featureGroupName))
+            {
+              Color fg = Color.black;
+              Color bg = Color.white;
+
+              return new ColumnCell(npfeat.description, fg, bg);
+            }
+          }
+        }
+      }
+      if (col.DbRefName != null)
+      {
+        for (DBRefEntryI dbr : seq.getDBRefs())
+        {
+          if (dbr.getSource().equals(col.DbRefName))
+          {
+            return new ColumnCell(dbr.getAccessionId(), Color.black,
+                    Color.white);
+          }
+        }
+      }
+    }
+    // no value for this sequence in given column
+    return null;
+  }
+
+  public IdColumn[] getIdColumns()
+  {
+    return columns.values().toArray(new IdColumn[0]);
+  }
+}