From d66fa7f908037c4bd6f4007911a86b0bdc6edcb4 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 23 Sep 2019 09:14:18 +0100
Subject: [PATCH] JAL-3070 javadoc for (mostly) jabaws specific methods

---
 .../ws/jws2/jabaws2/JabawsAnnotationInstance.java  |   56 +++++++++++++++++++-
 1 file changed, 55 insertions(+), 1 deletion(-)

diff --git a/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java b/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
index 95abe3c..3c269c4 100644
--- a/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
+++ b/src/jalview/ws/jws2/jabaws2/JabawsAnnotationInstance.java
@@ -125,11 +125,28 @@ public abstract class JabawsAnnotationInstance
             abstractJabaCalcWorker.getGapMap());
   }
 
+  /**
+   * service specific annotation creation method
+   * 
+   * @param running
+   * @param alignViewport
+   * @param gapMap
+   * @return
+   */
   abstract List<AlignmentAnnotation> annotationFromScoreManager(
           AnnotationWsJob running,
           AlignViewportI alignViewport, boolean[] gapMap);
 
-  // From JabawsCalcWorker
+  /**
+   * create and complete an annotation row from a JABAWS score object
+   * 
+   * @param alignViewport
+   * @param gapMap
+   * @param ourAnnot
+   * @param calcId
+   * @param alWidth
+   * @param scr
+   */
 
   protected void createAnnotationRowsForScores(AlignViewportI alignViewport,
           boolean[] gapMap, List<AlignmentAnnotation> ourAnnot,
@@ -148,6 +165,19 @@ public abstract class JabawsAnnotationInstance
     }
   }
 
+  /**
+   * create a sequence associated annotation row for JABAWS score object scr
+   * 
+   * @param alignViewport
+   * @param gapMap
+   * @param ourAnnot
+   * @param typeName
+   * @param calcId
+   * @param dseq
+   * @param base
+   * @param scr
+   * @return
+   */
   protected AlignmentAnnotation createAnnotationRowsForScores(
           AlignViewportI alignViewport, boolean[] gapMap,
           List<AlignmentAnnotation> ourAnnot, String typeName,
@@ -171,6 +201,20 @@ public abstract class JabawsAnnotationInstance
     return annotation;
   }
 
+  /**
+   * replace an existing sequence associated annotation with another, creating
+   * association as necessary
+   * 
+   * @param newAnnot
+   *          - annotation row used to create an instance on the dataset
+   *          sequence.
+   * @param typeName
+   *          - label used to match existing row
+   * @param calcId
+   *          - calcId for existing row
+   * @param aSeq
+   *          - alignment sequence with reference to destination dataet sequence
+   */
   protected void replaceAnnotationOnAlignmentWith(
           AlignmentAnnotation newAnnot, String typeName, String calcId,
           SequenceI aSeq)
@@ -195,6 +239,16 @@ public abstract class JabawsAnnotationInstance
     dssan.adjustForAlignment();
   }
 
+  /**
+   * create column annotation elements from Jabaws score object
+   * 
+   * @param gapMap
+   * @param annotation
+   * @param base
+   * @param alWidth
+   * @param scr
+   *          JABAWS score object
+   */
   protected void constructAnnotationFromScore(boolean[] gapMap,
           AlignmentAnnotation annotation,
           int base, int alWidth, Score scr)
-- 
1.7.10.2