From 601a323b3e90e2320c52d8b03aba55b1c535a9d0 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 10 Aug 2015 11:14:21 +0100 Subject: [PATCH] JAL-736 source formatting --- src/jalview/analysis/Conservation.java | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java index 1aa29e0..76323bc 100755 --- a/src/jalview/analysis/Conservation.java +++ b/src/jalview/analysis/Conservation.java @@ -20,10 +20,16 @@ */ package jalview.analysis; -import java.awt.Color; -import java.util.*; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; -import jalview.datamodel.*; +import java.awt.Color; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; /** * Calculates conservation values for a given set of sequences @@ -108,7 +114,7 @@ public class Conservation { for (s = 0; s < sSize; s++) { - sarray[s] = (SequenceI) sequences.get(s); + sarray[s] = sequences.get(s); if (sarray[s].getLength() > maxLength) { maxLength = sarray[s].getLength(); @@ -274,7 +280,7 @@ public class Conservation resultHash.put(type, ht.get("-")); } } - else if (((Integer) resultHash.get(type)).equals((Integer) ht + else if (((Integer) resultHash.get(type)).equals(ht .get(res)) == false) { resultHash.put(type, new Integer(-1)); @@ -373,7 +379,7 @@ public class Conservation { gapcons = countConsNGaps(i); totGaps = gapcons[1]; - pgaps = ((float) totGaps * 100) / (float) sequences.length; + pgaps = ((float) totGaps * 100) / sequences.length; consSymbs[i-start]=new String(); if (percentageGaps > pgaps) @@ -679,7 +685,7 @@ public class Conservation if (Character.isDigit(c)) { - value = (int) (c - '0'); + value = c - '0'; } else if (c == '*') { -- 1.7.10.2