From 51904e34c4fa66504e19ec0a984e4ce6d9031c44 Mon Sep 17 00:00:00 2001
From: soares <bsoares@dundee.ac.uk>
Date: Tue, 3 Mar 2020 20:40:03 +0000
Subject: [PATCH] JAL-3468 Adapted methods to report how many features have
 been dropped from the tooltip, and add final note to
 tooltip. Backward compatible methods left in.

---
 src/jalview/gui/SeqPanel.java                |   19 ++++--
 src/jalview/io/SequenceAnnotationReport.java |   87 ++++++++++++++++++++------
 2 files changed, 84 insertions(+), 22 deletions(-)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 75bf0cc..796d339 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1042,12 +1042,14 @@ public class SeqPanel extends JPanel
      * add features that straddle the gap (pos may be the residue before or
      * after the gap)
      */
+    int unshownFeatures = 0;
     if (av.isShowSequenceFeatures())
     {
       List<SequenceFeature> features = ap.getFeatureRenderer()
               .findFeaturesAtColumn(sequence, column + 1);
-      seqARep.appendFeatures(tooltipText, pos, features,
-              this.ap.getSeqPanel().seqCanvas.fr);
+      unshownFeatures = seqARep.appendFeaturesLengthLimit(tooltipText, pos,
+              features,
+              this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH);
 
       /*
        * add features in CDS/protein complement at the corresponding
@@ -1065,7 +1067,9 @@ public class SeqPanel extends JPanel
                   pos);
           if (mf != null)
           {
-            seqARep.appendFeatures(tooltipText, pos, mf, fr2);
+            unshownFeatures = seqARep.appendFeaturesLengthLimit(
+                    tooltipText, pos, mf, fr2,
+                    MAX_TOOLTIP_LENGTH);
           }
         }
       }
@@ -1080,7 +1084,14 @@ public class SeqPanel extends JPanel
       if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
       {
         tooltipText.setLength(MAX_TOOLTIP_LENGTH);
-        tooltipText.append("...");
+        tooltipText.append("...TOOLONG!");
+      }
+      if (unshownFeatures > 0)
+      {
+        tooltipText.append("<br/>").append("... ").append("<i>")
+                .append(unshownFeatures)
+                .append(" feature").append(unshownFeatures == 1 ? "" : "s")
+                .append(" not shown</i>");
       }
       String textString = tooltipText.toString();
       if (lastTooltip == null || !lastTooltip.equals(textString))
diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index df28ea3..9d82d66 100644
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -126,37 +126,65 @@ public class SequenceAnnotationReport
   }
 
   /**
-   * Append text for the list of features to the tooltip
+   * Append text for the list of features to the tooltip Returns number of
+   * features left if maxlength limit is (or would have been) reached
    * 
    * @param sb
    * @param residuePos
    * @param features
    * @param minmax
+   * @param maxlength
    */
-  public void appendFeatures(final StringBuilder sb, int residuePos,
-          List<SequenceFeature> features, FeatureRendererModel fr)
+  public int appendFeaturesLengthLimit(final StringBuilder sb,
+          int residuePos, List<SequenceFeature> features,
+          FeatureRendererModel fr, int maxlength)
   {
-    for (SequenceFeature feature : features)
+    for (int i = 0; i < features.size(); i++)
     {
-      appendFeature(sb, residuePos, fr, feature, null);
+      SequenceFeature feature = features.get(i);
+      if (appendFeature(sb, residuePos, fr, feature, null, maxlength))
+      {
+        return features.size() - i;
+      }
     }
+    return 0;
+  }
+
+  public void appendFeatures(final StringBuilder sb, int residuePos,
+          List<SequenceFeature> features, FeatureRendererModel fr)
+  {
+    appendFeaturesLengthLimit(sb, residuePos, features, fr, 0);
   }
 
   /**
    * Appends text for mapped features (e.g. CDS feature for peptide or vice versa)
+   * Returns number of features left if maxlength limit is (or would have been)
+   * reached
    * 
    * @param sb
    * @param residuePos
    * @param mf
    * @param fr
+   * @param maxlength
    */
-  public void appendFeatures(StringBuilder sb, int residuePos,
-          MappedFeatures mf, FeatureRendererModel fr)
+  public int appendFeaturesLengthLimit(StringBuilder sb, int residuePos,
+          MappedFeatures mf, FeatureRendererModel fr, int maxlength)
   {
-    for (SequenceFeature feature : mf.features)
+    for (int i = 0; i < mf.features.size(); i++)
     {
-      appendFeature(sb, residuePos, fr, feature, mf);
+      SequenceFeature feature = mf.features.get(i);
+      if (appendFeature(sb, residuePos, fr, feature, mf, maxlength))
+      {
+        return mf.features.size() - i;
+      }
     }
+    return 0;
+  }
+
+  public void appendFeatures(StringBuilder sb, int residuePos,
+          MappedFeatures mf, FeatureRendererModel fr)
+  {
+    appendFeaturesLengthLimit(sb, residuePos, mf, fr, 0);
   }
 
   /**
@@ -167,27 +195,28 @@ public class SequenceAnnotationReport
    * @param minmax
    * @param feature
    */
-  void appendFeature(final StringBuilder sb, int rpos,
+  boolean appendFeature(final StringBuilder sb0, int rpos,
           FeatureRendererModel fr, SequenceFeature feature,
-          MappedFeatures mf)
+          MappedFeatures mf, int maxlength)
   {
+    StringBuilder sb = new StringBuilder();
     if (feature.isContactFeature())
     {
       if (feature.getBegin() == rpos || feature.getEnd() == rpos)
       {
         if (sb.length() > 6)
         {
-          sb.append("<br>");
+          sb.append("<br/>");
         }
         sb.append(feature.getType()).append(" ").append(feature.getBegin())
                 .append(":").append(feature.getEnd());
       }
-      return;
+      return appendTextMaxLengthReached(sb0, sb, maxlength);
     }
 
-    if (sb.length() > 6)
+    if (sb0.length() > 6)
     {
-      sb.append("<br>");
+      sb.append("<br/>");
     }
     // TODO: remove this hack to display link only features
     boolean linkOnly = feature.getValue("linkonly") != null;
@@ -219,6 +248,7 @@ public class SequenceAnnotationReport
           description = description.substring(0, MAX_DESCRIPTION_LENGTH)
                   + ELLIPSIS;
         }
+
         sb.append("; ").append(description);
       }
 
@@ -259,6 +289,27 @@ public class SequenceAnnotationReport
         }
       }
     }
+    return appendTextMaxLengthReached(sb0, sb, maxlength);
+  }
+
+  void appendFeature(final StringBuilder sb, int rpos,
+          FeatureRendererModel fr, SequenceFeature feature,
+          MappedFeatures mf)
+  {
+    appendFeature(sb, rpos, fr, feature, mf, 0);
+  }
+
+  private static boolean appendTextMaxLengthReached(StringBuilder sb0,
+          StringBuilder sb, int maxlength)
+  {
+    boolean ret = false;
+    if (maxlength == 0 || sb0.length() + sb.length() < maxlength)
+    {
+      sb0.append(sb);
+      return false;
+    } else {
+      return true;
+    }
   }
 
   /**
@@ -475,7 +526,7 @@ public class SequenceAnnotationReport
       countForSource++;
       if (countForSource == 1 || !summary)
       {
-        sb.append("<br>");
+        sb.append("<br/>");
       }
       if (countForSource <= MAX_REFS_PER_SOURCE || !summary)
       {
@@ -501,11 +552,11 @@ public class SequenceAnnotationReport
     }
     if (moreSources)
     {
-      sb.append("<br>").append(source).append(COMMA).append(ELLIPSIS);
+      sb.append("<br/>").append(source).append(COMMA).append(ELLIPSIS);
     }
     if (ellipsis)
     {
-      sb.append("<br>(");
+      sb.append("<br/>(");
       sb.append(MessageManager.getString("label.output_seq_details"));
       sb.append(")");
     }
-- 
1.7.10.2