X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblFeatureLocations.java;h=a3c581d0306c89f954dd7c622eaf2672396e50cf;hb=c834ec02c02dec46f84960605bd7490aa8ac5a3a;hp=bbd394874c0ab2da599d69bece68dae47384fbfd;hpb=2ea52575d29eccae73a4262f52f59ff3fcf713b1;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
index bbd3948..a3c581d 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFeatureLocations.java
@@ -1,84 +1,84 @@
-package jalview.datamodel.xdb.embl;
-
-import java.util.Iterator;
-import java.util.Vector;
-
-public class EmblFeatureLocations {
-    Vector locElements;
-    String locationType;
-    boolean locationComplement;
-    /**
-     * @return the locationComplement
-     */
-    public boolean isLocationComplement() {
-        return locationComplement;
-    }
-    /**
-     * @param locationComplement the locationComplement to set
-     */
-    public void setLocationComplement(boolean locationComplement) {
-        this.locationComplement = locationComplement;
-    }
-    /**
-     * @return the locationType
-     */
-    public String getLocationType() {
-        return locationType;
-    }
-    /**
-     * @param locationType the locationType to set
-     */
-    public void setLocationType(String locationType) {
-        this.locationType = locationType;
-    }
-    /**
-     * @return the locElements
-     */
-    public Vector getLocElements() {
-        return locElements;
-    }
-    /**
-     * @param locElements the locElements to set
-     */
-    public void setLocElements(Vector locElements) {
-        this.locElements = locElements;
-    }
-    /**
-     * Return all location elements as start-end pairs on referenced sequence 
-     * TODO: pass back complement and 'less than or more than' range information
-     * @return int[] { start1, end1, ... }
-     */
-    public int[] getElementRanges() {
-        if (locationType.equalsIgnoreCase("single")) {
-            int[] se = new int[locElements.size()*2];            
-            int sepos=0;
-            for (Iterator le=locElements.iterator();le.hasNext();) {
-                EmblFeatureLocElement loce = (EmblFeatureLocElement) le.next();
-                BasePosition bp[] = loce.getBasePositions();
-                if (bp.length==2) {
-                    se[sepos++] = Integer.parseInt(bp[0].getPos());
-                    se[sepos++] = Integer.parseInt(bp[1].getPos());
-                }
-            }
-            return se;
-        }
-        if (locationType.equalsIgnoreCase("join")) {
-            int[] se = new int[locElements.size()*2];            
-            int sepos=0;
-            for (Iterator le=locElements.iterator();le.hasNext();) {
-                EmblFeatureLocElement loce = (EmblFeatureLocElement) le.next();
-                BasePosition bp[] = loce.getBasePositions();
-                if (bp.length==2) {
-                    se[sepos++] = Integer.parseInt(bp[0].getPos());
-                    se[sepos++] = Integer.parseInt(bp[1].getPos());
-                }
-            }
-            return se;
-        }
-        if (locationType!=null)
-        {
-          jalview.bin.Cache.log.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
-        }
-        return null;
-    }
+package jalview.datamodel.xdb.embl;
+
+import java.util.Iterator;
+import java.util.Vector;
+
+public class EmblFeatureLocations {
+    Vector locElements;
+    String locationType;
+    boolean locationComplement;
+    /**
+     * @return the locationComplement
+     */
+    public boolean isLocationComplement() {
+        return locationComplement;
+    }
+    /**
+     * @param locationComplement the locationComplement to set
+     */
+    public void setLocationComplement(boolean locationComplement) {
+        this.locationComplement = locationComplement;
+    }
+    /**
+     * @return the locationType
+     */
+    public String getLocationType() {
+        return locationType;
+    }
+    /**
+     * @param locationType the locationType to set
+     */
+    public void setLocationType(String locationType) {
+        this.locationType = locationType;
+    }
+    /**
+     * @return the locElements
+     */
+    public Vector getLocElements() {
+        return locElements;
+    }
+    /**
+     * @param locElements the locElements to set
+     */
+    public void setLocElements(Vector locElements) {
+        this.locElements = locElements;
+    }
+    /**
+     * Return all location elements as start-end pairs on referenced sequence 
+     * TODO: pass back complement and 'less than or more than' range information
+     * @return int[] { start1, end1, ... }
+     */
+    public int[] getElementRanges() {
+        if (locationType.equalsIgnoreCase("single")) {
+            int[] se = new int[locElements.size()*2];            
+            int sepos=0;
+            for (Iterator le=locElements.iterator();le.hasNext();) {
+                EmblFeatureLocElement loce = (EmblFeatureLocElement) le.next();
+                BasePosition bp[] = loce.getBasePositions();
+                if (bp.length==2) {
+                    se[sepos++] = Integer.parseInt(bp[0].getPos());
+                    se[sepos++] = Integer.parseInt(bp[1].getPos());
+                }
+            }
+            return se;
+        }
+        if (locationType.equalsIgnoreCase("join")) {
+            int[] se = new int[locElements.size()*2];            
+            int sepos=0;
+            for (Iterator le=locElements.iterator();le.hasNext();) {
+                EmblFeatureLocElement loce = (EmblFeatureLocElement) le.next();
+                BasePosition bp[] = loce.getBasePositions();
+                if (bp.length==2) {
+                    se[sepos++] = Integer.parseInt(bp[0].getPos());
+                    se[sepos++] = Integer.parseInt(bp[1].getPos());
+                }
+            }
+            return se;
+        }
+        if (locationType!=null)
+        {
+          jalview.bin.Cache.log.error("EmbleFeatureLocations.getElementRanges cannot deal with locationType=='"+locationType+"'");
+        }
+        return null;
+    }
 }
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