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jernst98 committed Sep 3, 2021
1 parent 515c2bf commit dcfd87b
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Showing 9 changed files with 526 additions and 288 deletions.
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56 changes: 28 additions & 28 deletions edu/mit/compbio/ChromHMM/BrowserOutput.java
Original file line number Diff line number Diff line change
Expand Up @@ -159,8 +159,8 @@ private void makeColorMapping() throws IOException
while ((szLine = brcolor.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szID = st.nextToken();
String szColor = st.nextToken();
String szID = st.nextToken().trim();
String szColor = st.nextToken().trim();
hmcolor.put(szID, szColor);
}
brcolor.close();
Expand Down Expand Up @@ -347,8 +347,8 @@ private void makeLabelMapping() throws IOException
while ((szLine = bridlabel.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szID = st.nextToken();
String szLabelExtend = st.nextToken();
String szID = st.nextToken().trim();
String szLabelExtend = st.nextToken().trim();
hmlabelExtend.put(szID,szLabelExtend);
}
bridlabel.close();
Expand Down Expand Up @@ -378,10 +378,10 @@ public void makebrowserdense() throws IOException
while ((szLine =brsegment.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szcurrchrom = st.nextToken();
int nbegin = Integer.parseInt(st.nextToken());
int nend = Integer.parseInt(st.nextToken());
String szFullID = st.nextToken();
String szcurrchrom = st.nextToken().trim();
int nbegin = Integer.parseInt(st.nextToken().trim());
int nend = Integer.parseInt(st.nextToken().trim());
String szFullID = st.nextToken().trim();
String szID = szFullID.substring(1); //this removes ordering type
if (bfirst)
{
Expand Down Expand Up @@ -426,10 +426,10 @@ public void makebrowserdense() throws IOException
while ((szLine =brsegment.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szcurrchrom = st.nextToken();
int nbegin = Integer.parseInt(st.nextToken());
int nend = Integer.parseInt(st.nextToken());
String szFullID = st.nextToken();
String szcurrchrom = st.nextToken().trim();
int nbegin = Integer.parseInt(st.nextToken().trim());
int nend = Integer.parseInt(st.nextToken().trim());
String szFullID = st.nextToken().trim();
String szID = szFullID.substring(1); //this removes ordering type
if (bfirst)
{
Expand Down Expand Up @@ -496,10 +496,10 @@ public void makebrowserexpanded() throws IOException
while ((szLine = brsegment.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szchrom = st.nextToken();
int nbegin = Integer.parseInt(st.nextToken());
int nend = Integer.parseInt(st.nextToken());
szLabelFull = st.nextToken();
String szchrom = st.nextToken().trim();
int nbegin = Integer.parseInt(st.nextToken().trim());
int nend = Integer.parseInt(st.nextToken().trim());
szLabelFull = st.nextToken().trim();
String szLabel = szLabelFull.substring(1);

hmlabelToFull.put(szLabel, szLabelFull);
Expand Down Expand Up @@ -740,10 +740,10 @@ public void makebrowserexpandedLowMem() throws IOException
while ((szLine = brsegment.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szchrom = st.nextToken();
int nbegin = Integer.parseInt(st.nextToken());
int nend = Integer.parseInt(st.nextToken());
szLabelFull = st.nextToken();
String szchrom = st.nextToken().trim();
int nbegin = Integer.parseInt(st.nextToken().trim());
int nend = Integer.parseInt(st.nextToken().trim());
szLabelFull = st.nextToken().trim();
String szLabel = szLabelFull.substring(1);

hmlabelToFull.put(szLabel, szLabelFull);
Expand Down Expand Up @@ -827,12 +827,12 @@ public void makebrowserexpandedLowMem() throws IOException
while ((szLine = brsegment.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szchrom = st.nextToken();
String szchrom = st.nextToken().trim();
if (szchrom.equals(szcurrchrom))
{
int nbegin = Integer.parseInt(st.nextToken());
int nend = Integer.parseInt(st.nextToken());
szLabelFull = st.nextToken();
int nbegin = Integer.parseInt(st.nextToken().trim());
int nend = Integer.parseInt(st.nextToken().trim());
szLabelFull = st.nextToken().trim();
String szLabel = szLabelFull.substring(1);

ArrayList alRecs = (ArrayList) hmcoords.get(szLabel);
Expand Down Expand Up @@ -930,12 +930,12 @@ public void makebrowserexpandedLowMem() throws IOException
while ((szLine = brsegment.readLine())!=null)
{
StringTokenizer st = new StringTokenizer(szLine,"\t");
String szchrom = st.nextToken();
String szchrom = st.nextToken().trim();
if (szchrom.equals(szcurrchrom))
{
int nbegin = Integer.parseInt(st.nextToken());
int nend = Integer.parseInt(st.nextToken());
szLabelFull = st.nextToken();
int nbegin = Integer.parseInt(st.nextToken().trim());
int nend = Integer.parseInt(st.nextToken().trim());
szLabelFull = st.nextToken().trim();
String szLabel = szLabelFull.substring(1);

ArrayList alRecs = (ArrayList) hmcoords.get(szLabel);
Expand Down
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