JAL-3026 srcjar files for VARNA and log4j

[jalview.git] / srcjar / fr / orsay / lri / varna / models / templates / DrawRNATemplateMethod.java

diff --git a/srcjar/fr/orsay/lri/varna/models/templates/DrawRNATemplateMethod.java b/srcjar/fr/orsay/lri/varna/models/templates/DrawRNATemplateMethod.java
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+++ b/srcjar/fr/orsay/lri/varna/models/templates/DrawRNATemplateMethod.java
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+/**
+ * File written by Raphael Champeimont
+ * UMR 7238 Genomique des Microorganismes
+ */
+package fr.orsay.lri.varna.models.templates;
+
+/**
+ * What to do in case some helices are of a different length
+ * in the template and the actual helix.
+ * Possibles values are:
+ * 0 - No adjustment is done.
+ *     A longer than expected helix might bump into an other helix.
+ * 1 - Scaling factors (actual length / template length) are calculated,
+ *     the maximum scaling factor L is extracted, then all helix positions
+ *     are multiplied by L. 
+ * 2 - Same as 1, but L is computed as the minimum value such that there
+ *     are no backbone intersections.
+ */
+public enum DrawRNATemplateMethod {
+       NOADJUST("No Adjust"), MAXSCALINGFACTOR("Max Scaling"), NOINTERSECT("Non-crossing"), HELIXTRANSLATE("Helix Translation");
+       
+       String _msg;
+       
+       public static DrawRNATemplateMethod getDefault() {
+               return HELIXTRANSLATE;
+       }
+       
+
+       public String toString()
+       {
+               return _msg;
+       }
+       
+       private DrawRNATemplateMethod(String msg)
+       {
+               _msg = msg;
+       }
+}
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