From 06f7fc9313488587d9c0158b830ff66a68336ce3 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 10 Nov 2017 16:37:35 +0000 Subject: [PATCH] JAL-2828 refactored duplicate code for searching lists of AlignmentAnnotation to static methods. --- src/jalview/datamodel/Alignment.java | 17 ++---- src/jalview/datamodel/AlignmentAnnotation.java | 66 ++++++++++++++++++++++++ src/jalview/datamodel/SequenceGroup.java | 45 +++------------- 3 files changed, 76 insertions(+), 52 deletions(-) diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 8c5e4ac..77667b9 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -28,6 +28,7 @@ import jalview.util.LinkedIdentityHashSet; import jalview.util.MessageManager; import java.util.ArrayList; +import java.util.Arrays; import java.util.Collections; import java.util.Enumeration; import java.util.HashSet; @@ -1637,20 +1638,8 @@ public class Alignment implements AlignmentI public Iterable findAnnotations(SequenceI seq, String calcId, String label) { - ArrayList aa = new ArrayList<>(); - for (AlignmentAnnotation ann : getAlignmentAnnotation()) - { - if ((calcId == null || (ann.getCalcId() != null - && ann.getCalcId().equals(calcId))) - && (seq == null || (ann.sequenceRef != null - && ann.sequenceRef == seq)) - && (label == null - || (ann.label != null && ann.label.equals(label)))) - { - aa.add(ann); - } - } - return aa; + return AlignmentAnnotation.findAnnotations( + Arrays.asList(getAlignmentAnnotation()), seq, calcId, label); } @Override diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 09facbf..ffc3105 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -24,6 +24,7 @@ import jalview.analysis.Rna; import jalview.analysis.SecStrConsensus.SimpleBP; import jalview.analysis.WUSSParseException; +import java.util.ArrayList; import java.util.Collection; import java.util.Collections; import java.util.HashMap; @@ -1471,4 +1472,69 @@ public class AlignmentAnnotation { return graphMin < graphMax; } + + public static Iterable findAnnotations( + Iterable list, SequenceI seq, String calcId, + String label) + { + + ArrayList aa = new ArrayList<>(); + for (AlignmentAnnotation ann : list) + { + if ((calcId == null || (ann.getCalcId() != null + && ann.getCalcId().equals(calcId))) + && (seq == null || (ann.sequenceRef != null + && ann.sequenceRef == seq)) + && (label == null + || (ann.label != null && ann.label.equals(label)))) + { + aa.add(ann); + } + } + return aa; + } + + /** + * Answer true if any annotation matches the calcId passed in (if not null). + * + * @param list + * annotation to search + * @param calcId + * @return + */ + public static boolean hasAnnotation(List list, + String calcId) + { + + if (calcId != null && !"".equals(calcId)) + { + for (AlignmentAnnotation a : list) + { + if (a.getCalcId() == calcId) + { + return true; + } + } + } + return false; + } + + public static Iterable findAnnotation( + List list, String calcId) + { + + List aa = new ArrayList<>(); + if (calcId == null) + { + return aa; + } + for (AlignmentAnnotation a : list) + { + if (calcId.equals(a.getCalcId())) + { + aa.add(a); + } + } + return aa; + } } diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index e2f15e1..6b797d7 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -30,6 +30,7 @@ import java.awt.Color; import java.beans.PropertyChangeListener; import java.beans.PropertyChangeSupport; import java.util.ArrayList; +import java.util.Arrays; import java.util.List; import java.util.Map; @@ -1316,39 +1317,16 @@ public class SequenceGroup implements AnnotatedCollectionI @Override public Iterable findAnnotation(String calcId) { - List aa = new ArrayList<>(); - if (calcId == null) - { - return aa; - } - for (AlignmentAnnotation a : getAlignmentAnnotation()) - { - if (calcId.equals(a.getCalcId())) - { - aa.add(a); - } - } - return aa; + return AlignmentAnnotation.findAnnotation( + Arrays.asList(getAlignmentAnnotation()), calcId); } @Override public Iterable findAnnotations(SequenceI seq, String calcId, String label) { - ArrayList aa = new ArrayList<>(); - for (AlignmentAnnotation ann : getAlignmentAnnotation()) - { - if ((calcId == null || (ann.getCalcId() != null - && ann.getCalcId().equals(calcId))) - && (seq == null || (ann.sequenceRef != null - && ann.sequenceRef == seq)) - && (label == null - || (ann.label != null && ann.label.equals(label)))) - { - aa.add(ann); - } - } - return aa; + return AlignmentAnnotation.findAnnotations( + Arrays.asList(getAlignmentAnnotation()), seq, calcId, label); } /** @@ -1359,17 +1337,8 @@ public class SequenceGroup implements AnnotatedCollectionI */ public boolean hasAnnotation(String calcId) { - if (calcId != null && !"".equals(calcId)) - { - for (AlignmentAnnotation a : getAlignmentAnnotation()) - { - if (a.getCalcId() == calcId) - { - return true; - } - } - } - return false; + return AlignmentAnnotation + .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId); } /** -- 1.7.10.2