ascii type

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblFeatureLocations.java

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