From 5b5f8e29848922d38d2d7ee3900c76f894861d7f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Thu, 12 Feb 2009 11:10:03 +0000
Subject: [PATCH] - added gap thresholding
---
.../exmo/align/impl/BasicAlignment.java | 17 ++++++++++++++++-
1 file changed, 16 insertions(+), 1 deletion(-)
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index 3e665182..080abcb5 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2008
+ * Copyright (C) INRIA, 2003-2009
* Copyright (C) CNR Pisa, 2005
*
* This program is free software; you can redistribute it and/or modify
@@ -416,6 +416,8 @@ public class BasicAlignment implements Alignment {
* - getting those cells with strength at worse n under the best (span)
* - getting the n% best cells (perc)
* - getting those cells with strength at worse n% of the best (prop)
+ * - getting all cells until a gap of n (hardgap)
+ * - getting all cells until a gap of n% of the last (propgap)
* Rule:
* threshold is betweew 1 and 0
**************************************************************************/
@@ -436,6 +438,19 @@ public class BasicAlignment implements Alignment {
i = (new Double(size*threshold)).intValue();
} else if ( method.equals("best") ){
i = new Double(threshold*100).intValue();
+ } else if ( method.equals("hardgap") || method.equals("propgap") ){
+ double gap;
+ double last = ((Cell)buffer.get(0)).getStrength();
+ if ( method.equals("propgap") ) gap = last * threshold;
+ else gap = threshold;
+ for( i=1; i < size && !found ;) {
+ if ( last - ((Cell)buffer.get(i)).getStrength() > gap ) found = true;
+ else {
+ last = ((Cell)buffer.get(i)).getStrength();
+ if ( method.equals("propgap") ) gap = last * threshold;
+ i++;
+ }
+ }
} else {
double max;
if ( method.equals("hard") ) max = threshold;
--
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