JAL-1260 v2 patch from David Roldán-Martínez

[jalview.git] / src / jalview / io / xdb / genbank / GenBankLocations.java

diff --git a/src/jalview/io/xdb/genbank/GenBankLocations.java b/src/jalview/io/xdb/genbank/GenBankLocations.java
new file mode 100644 (file)
index 0000000..ae3e47b
--- /dev/null
+++ b/src/jalview/io/xdb/genbank/GenBankLocations.java
@@ -0,0 +1,98 @@
+package jalview.io.xdb.genbank;
+
+/**
+ *
+ * @author Dieval Guizelini
+ */
+public class GenBankLocations extends GenBankLocation {
+    public static final int NONE = 1; // default
+    public static final int COMPLEMENT = 2;
+    public static final int JOIN = 3;
+    public static final int ORDER = 4; // conj com ordem desconhecida
+    private int operator = NONE;
+    private java.util.List<GenBankLocation> units;
+
+    public GenBankLocations() {
+        units = new java.util.ArrayList<GenBankLocation>();
+    }
+
+    @Override
+    public void setComplement(boolean complement){
+        super.setComplement(complement);
+        this.operator = COMPLEMENT;
+        if (units != null) {
+            for (GenBankLocation o : units) {
+                o.setComplement(complement);
+            }
+        }
+    }
+
+    @Override
+    public String toString() {
+        StringBuilder sb = new StringBuilder();
+        if (getOperator() == COMPLEMENT) {
+            sb.append("complement(");
+        } else if (getOperator() == JOIN) {
+            sb.append("join(");
+        } else if (getOperator() == ORDER) {
+            sb.append("order(");
+        }
+        if (units.size() > 0) {
+            sb.append(units.get(0).toString());
+            for (int i = 1; i < units.size(); i++) {
+                sb.append(",");
+                sb.append(units.get(i).toString());
+            }
+        }
+        if (getOperator() != NONE) {
+            sb.append(")");
+        }
+        return sb.toString();
+    }
+
+    /**
+     * @return the units
+     */
+    public java.util.List<GenBankLocation> getUnits() {
+        return units;
+    }
+
+    /**
+     * @param units the units to set
+     */
+    public void setUnits(java.util.List<GenBankLocation> units) {
+        this.units = units;
+    }
+
+    @Override
+    public int getMinor() {
+        if( units.size() > 0 ) {
+            return units.get(0).getMinor();
+        }
+        return 0;
+    }
+
+    @Override
+    public int getMajor() {
+        int ind = units.size();
+        if( ind > 0 ) {
+            return units.get(ind-1).getMajor();
+        }
+        return 0;
+    }
+
+    /**
+     * @return the operator
+     */
+    public int getOperator() {
+        return operator;
+    }
+
+    /**
+     * @param operator the operator to set
+     */
+    public void setOperator(int operator) {
+        this.operator = operator;
+    }
+
+}