X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=bc8d0cf1d1723e423b1d1d62608ce1a62d2bb6fa;hb=2eea4e73351d902cd88923d863e9780fa57a0ee7;hp=11e77d85a138ec545ddbd37c4287ce30ccdb0e7f;hpb=9a0e53e18ba1280658e1424c5e08b90e7beeebde;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 11e77d8..bc8d0cf 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -23,10 +23,15 @@ package jalview.datamodel;
import jalview.api.DBRefEntryI;
import java.util.Arrays;
+import java.util.List;
public class DBRefEntry implements DBRefEntryI
{
- String source = "", version = "", accessionId = "";
+ String source = "";
+
+ String version = "";
+
+ String accessionId = "";
/**
* maps from associated sequence to the database sequence's coordinate system
@@ -67,10 +72,10 @@ public class DBRefEntry implements DBRefEntryI
public DBRefEntry(DBRefEntryI entry)
{
this((entry.getSource() == null ? "" : new String(entry.getSource())),
- (entry.getVersion() == null ? "" : new String(
- entry.getVersion())),
- (entry.getAccessionId() == null ? "" : new String(
- entry.getAccessionId())),
+ (entry.getVersion() == null ? ""
+ : new String(entry.getVersion())),
+ (entry.getAccessionId() == null ? ""
+ : new String(entry.getAccessionId())),
(entry.getMap() == null ? null : new Mapping(entry.getMap())));
}
@@ -88,9 +93,8 @@ public class DBRefEntry implements DBRefEntryI
{
return true;
}
- if (equalRef(entry)
- && ((map == null && entry.map == null) || (map != null
- && entry.map != null && map.equals(entry.map))))
+ if (equalRef(entry) && ((map == null && entry.map == null)
+ || (map != null && entry.map != null && map.equals(entry.map))))
{
return true;
}
@@ -103,7 +107,8 @@ public class DBRefEntry implements DBRefEntryI
*
* - source and accession are identical (ignoring case)
* - version is identical (ignoring case), or this version is of the format
- * "someSource:0", in which case the version for the other entry replaces it
+ * "someSource:0", in which case the version for the other entry replaces
+ * it
* - mappings are not compared but if this entry has no mapping, replace
* with that for the other entry
*
@@ -140,8 +145,8 @@ public class DBRefEntry implements DBRefEntryI
String otherAccession = other.getAccessionId();
if ((accessionId == null && otherAccession != null)
|| (accessionId != null && otherAccession == null)
- || (accessionId != null && !accessionId
- .equalsIgnoreCase(otherAccession)))
+ || (accessionId != null
+ && !accessionId.equalsIgnoreCase(otherAccession)))
{
return false;
}
@@ -159,9 +164,8 @@ public class DBRefEntry implements DBRefEntryI
}
else
{
- if (version != null
- && (otherVersion == null || !version
- .equalsIgnoreCase(otherVersion)))
+ if (version != null && (otherVersion == null
+ || !version.equalsIgnoreCase(otherVersion)))
{
return false;
}
@@ -196,12 +200,12 @@ public class DBRefEntry implements DBRefEntryI
return true;
}
if (entry != null
- && (source != null && entry.getSource() != null && source
- .equalsIgnoreCase(entry.getSource()))
- && (accessionId != null && entry.getAccessionId() != null && accessionId
- .equalsIgnoreCase(entry.getAccessionId()))
- && (version != null && entry.getVersion() != null && version
- .equalsIgnoreCase(entry.getVersion())))
+ && (source != null && entry.getSource() != null
+ && source.equalsIgnoreCase(entry.getSource()))
+ && (accessionId != null && entry.getAccessionId() != null
+ && accessionId.equalsIgnoreCase(entry.getAccessionId()))
+ && (version != null && entry.getVersion() != null
+ && version.equalsIgnoreCase(entry.getVersion())))
{
return true;
}
@@ -281,7 +285,7 @@ public class DBRefEntry implements DBRefEntryI
}
@Override
- public boolean isPrimary()
+ public boolean isPrimaryCandidate()
{
/*
* if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference.
@@ -297,12 +301,15 @@ public class DBRefEntry implements DBRefEntryI
{
return false;
}
- // check map is really 1:1, no shifts allowed.
- if (map.getMap().getFromHighest() != map.getMap().getToHighest()
- && map.getMap().getFromLowest() != map.getMap().getToLowest()
- && !Arrays.equals(
- map.getMap().getFromRanges().toArray(new int[0][]),
- map.getMap().getToRanges().toArray(new int[0][])))
+ // check map is between identical single contiguous ranges
+ List fromRanges = map.getMap().getFromRanges();
+ List toRanges = map.getMap().getToRanges();
+ if (fromRanges.size() != 1 || toRanges.size() != 1)
+ {
+ return false;
+ }
+ if (fromRanges.get(0)[0] != toRanges.get(0)[0]
+ || fromRanges.get(0)[1] != toRanges.get(0)[1])
{
return false;
}