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v4.0.4
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‎docs/Release.html‎

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@@ -61,7 +61,7 @@
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There have been many improvements, but the following provides some recent critical points.
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<font size="2">
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<table>
64-
<tr><td><a href="#v403">v4.0.3</a><td>14-July-22<td><ttp>All<td>Small improvements.
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<tr><td><a href="#v403">v4.0.4</a><td>29-July-22<td><ttp>All<td>Small improvements.
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<tr><td><a href="#v339">v3.3.9</a><td>27-Dec-21<td><ttp><ttp>runAS</ttp></ttp><td>Improved interface for full subset UniProt; updated Demo.
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<tr><td><a href="#v335">v3.3.5</a><td>04-Nov-21<td><ttp>viewSingle</ttp><td>log2FC TPM analysis
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<tr><td><a href="#v334">v3.3.4</a><td>18-Oct-21<td><ttp>runSingle</ttp><td><ttl>ORF finder</ttl> improvements
@@ -76,6 +76,14 @@
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</table>
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</font>
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79+
<a id=v404></a>
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<h4>v4.0.4 29-July-2022</h4>
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The last tar file had "._" MacOS files, which have been removed from this release.
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<ul>
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<li><u>Overviews</u>: The HTML Overview files conform to HTML5.
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<li><u>Startup</u>: All programs show the same banners on startup, including memory and Java version.
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<li><u>Execute</u>: All programs clearly show log file and size of it.
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</ul>
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<a id=v403></a>
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<h4>v4.0.3 14-July-2022</h4>
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‎docs/index.html‎

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@@ -60,7 +60,7 @@
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TCW uses Java, mySQL, optionally R, and various <a href="./External.html">External</a> packages.
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It has been tested on Linux and Mac.
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<ul>
63-
<li>Last release: TCW v4.0.3 (14-July-22). See <a href="./Release.html">Release Notes</a>.
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<li>Last release: TCW v4.0.4 (29-July-22). See <a href="./Release.html">Release Notes</a>.
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Published in <a href="https://doi.org/10.1101/733311" class="ext" target="_blank">BioRxiv</a> (02-May-2022).
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‎docs/ov/sDemo.html‎

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@@ -3,7 +3,7 @@
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<body>
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<center>
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<h2>Overview for sTCW_demoTra </h2>
6-
<table width=700 border=1><tr><td>
6+
<table style="width: 800px; border: 2px solid #999999;"><tr><td>
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<pre>
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Project: tra #Seqs: 211 #Hits: 12,296 #GOs: 6,144 TPM Seq-DE GO-Enrich Pairs
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‎execAnno‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,4 @@
11
#!/bin/sh
2-
java -Xmx8192m -classpath java/jars/stcw.jar:jpave/jars/mysql-connector-java-5.0.5-bin.jar sng.annotator.runSTCWMain $@
2+
mem="8192m";
3+
echo ">>>> execAnno ($mem) `date` <<<<"
4+
java -Xmx$mem -classpath java/jars/stcw.jar:jpave/jars/mysql-connector-java-5.0.5-bin.jar sng.annotator.runSTCWMain $@

‎execAssm‎

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Original file line numberDiff line numberDiff line change
@@ -1,2 +1,4 @@
11
#!/bin/sh
2-
java -Xmx8192m -classpath java/jars/stcw.jar:jpave/jars/mysql-connector-java-5.0.5-bin.jar sng.assem.AssemMain $@
2+
mem="8192m";
3+
echo ">>>> execAssm (Instantiate) ($mem) `date` <<<<"
4+
java -Xmx$mem -classpath java/jars/stcw.jar:jpave/jars/mysql-connector-java-5.0.5-bin.jar sng.assem.AssemMain $@

‎execLoadLib‎

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Original file line numberDiff line numberDiff line change
@@ -1,2 +1,4 @@
11
#!/bin/sh
2-
java -Xmx8192m -classpath java/jars/stcw.jar:jpave/jars/mysql-connector-java-5.0.5-bin.jar sng.assem.LoadLibMain $@
2+
mem="8192m";
3+
echo ">>>> execLoadLib ($mem) `date` <<<<"
4+
java -Xmx$mem -classpath java/jars/stcw.jar:jpave/jars/mysql-connector-java-5.0.5-bin.jar sng.assem.LoadLibMain $@

‎java/README‎

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,9 @@
11
tar xvf classes_ext.tar.gz
2+
23
# Edit top line of Makefile to set JAVA_PATH
34
make
45

5-
Download TCW_4.tar.gz, and extract the /Ext directory to put under the TCW_4
6-
directory. This contains the external programs used by TCW.
6+
# Download TCW_4.tar.gz, and put the following two in the TCW_4 directory:
7+
# the /Ext directory, which contains the external programs used by TCW.
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# the /projects directory, which contains the demo files
9+
# and provides the data directory structure.

‎java/src/cmp/compile/Summary.java‎

Lines changed: 26 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -95,7 +95,7 @@ public String updateSummary() {
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text += lines.get(i) + "\n";
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9797
mDB.executeUpdate("UPDATE info SET summary = \"" + text + "\"");
98-
writeOverview(text);
98+
writeHTML(text);
9999
Out.PrtSpMsg(0, "Complete overview");
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}
101101
catch (Exception e) {ErrorReport.die(e, "create/get summary");}
@@ -632,26 +632,44 @@ private void makeProcessing() {
632632
catch (Exception e) {ErrorReport.prtReport(e, "processing");}
633633
}
634634

635-
public void writeOverview(String text) {
635+
// HTML CAS404 make html pass BBEdit test
636+
public void writeHTML(String text) {
636637
String projDir = Globals.PROJECTDIR;
637638
String sumDir = Globals.summaryPath;
638639
String overFilePath = sumDir + "/" + dbName + ".html";
639640
try {
640641
if (!new File(projDir).exists()) return; // should exist
641642

643+
String [] lines = text.split("\n");
644+
for (int i=0; i<lines.length; i++) {
645+
lines[i] = lines[i].replaceAll("&", "&amp;");
646+
lines[i] = lines[i].replaceAll(">", "&gt;");
647+
lines[i] = lines[i].replaceAll("<", "&lt;");
648+
}
649+
642650
File h = new File(sumDir);
643651
if (!h.exists()) {
644652
System.out.println("Creating directory " + sumDir);
645653
h.mkdir();
646654
}
647655
FileOutputStream out = new FileOutputStream(overFilePath);
648656
PrintWriter fileObj = new PrintWriter(out);
649-
// CAS310 make centered table
650-
String head = "<html><title>mTCW_" + dbName + " overview</title><body><center>"
651-
+ "\n<h2>mTCW overview for " + dbName + "</h2>"
652-
+ "\n<table width=600 border=1><tr><td><pre>";
653-
String foot = "\n</pre></table></body></html>";
654-
fileObj.println(head + text + foot);
657+
658+
Out.prtSp(1, "Writing overview HTML file: " + overFilePath);
659+
660+
fileObj.println("<!DOCTYPE html>"); // CAS404 html5
661+
fileObj.println("<html>");
662+
fileObj.println("<head><title>Overview mTCW_" + dbName + "</title></head>");
663+
fileObj.println("<body>");
664+
fileObj.println("<center>");
665+
fileObj.println("<h2>Overview for mTCW_" + dbName + " </h2>");
666+
fileObj.println("<table style=\"width: 800px; border: 2px solid #999999;\"><tr><td>");
667+
fileObj.println("<pre>");
668+
for (int i=0; i<lines.length; i++) fileObj.println(lines[i]);
669+
fileObj.println("</pre>");
670+
671+
fileObj.println("</table></center></body>");
672+
fileObj.println("</html>");
655673
fileObj.close();
656674
}
657675
catch (Exception e){ErrorReport.prtReport(e, "Error writing to " + overFilePath);}

‎java/src/cmp/compile/panels/BlastPanel.java‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -113,14 +113,15 @@ public void actionPerformed(ActionEvent arg0) {
113113
* Add blast pairs
114114
*/
115115
public void createPairsFromBlast() {
116+
Out.prtHeader("Add pairs");
116117
Out.createLogFile(theCompilePanel.getCurProjAbsDir(), Globals.searchFile);
117118

118119
if (theCompilePanel.getDBInfo().getCntPair()>0) {
119120
UserPrompt.showMsg("Pairs exist already");
120121
return;
121122
}
122123
try {
123-
Out.PrtDateMsg("Create pairs from search result files");
124+
Out.PrtTimeMsg("Create pairs from search result files");
124125
long time = Out.getTime();
125126

126127
Pairwise pw = new Pairwise(theCompilePanel);
@@ -148,6 +149,7 @@ public void createPairsFromBlast() {
148149
}
149150

150151
public void runBlast() {
152+
Out.prtHeader("Run Search");
151153
Out.createLogFile(theCompilePanel.getCurProjAbsDir(), Globals.searchFile);
152154

153155
String blastDir = theCompilePanel.getCurProjAbsDir() + "/" + Globals.Search.BLASTDIR;

‎java/src/cmp/compile/panels/CompileFrame.java‎

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@@ -37,7 +37,7 @@ public CompileFrame(runMTCWMain parent) {
3737
private void runMultiTCW() {
3838
Vector<String> hostNames = new Vector<String>();
3939
hostNames.add(hostsObj.host());
40-
setTitle("runMultiTCW " + Globalx.strTCWver);
40+
setTitle("runMultiTCW v" + Globalx.strTCWver);
4141

4242
setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
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