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Minor bugfixes #9

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Minor bugfixes #9

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8c65f89
Fix line endings.
markwoon Feb 10, 2016
4191434
Remove obsolete file.
markwoon Feb 10, 2016
5be7d91
Tweak publication xref string. Include PMID.
markwoon Aug 21, 2015
6ab28df
Avoid ConcurrentModificationException.
markwoon Aug 21, 2015
39c1db7
Delete build directory on dist-clean.
markwoon Aug 21, 2015
c965fe2
Avoid NPE. Should never happen, and yet it does.
markwoon Feb 8, 2016
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1 change: 1 addition & 0 deletions build.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,7 @@
<delete file="wikipathways-client.jar"/>
<delete dir="${release.dir}" />
<delete dir="${axis.wpclient.dir}" />
<delete dir="build" />
<iterate target="dist-clean"/>
</target>

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59 changes: 36 additions & 23 deletions modules/org.pathvisio.core/src/org/pathvisio/core/biopax/PublicationXref.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@
//
package org.pathvisio.core.biopax;

import org.pathvisio.core.util.Utils;

import java.util.ArrayList;
import java.util.List;

Expand Down Expand Up @@ -152,37 +154,48 @@ public String toHTML() {
}

public String toString() {
StringBuilder builder = new StringBuilder();
String title = getTitle();
String pmid = getPubmedId();
String authors = getAuthorString();
String source = getSource();
String year = getYear();
if(title != null && title.length() > 0) {
title += "; ";
} else {
title = "";
if(!Utils.isEmpty(title)) {
builder.append(title);
if (!title.endsWith(".") && title.endsWith("!") && title.endsWith("?")) {
builder.append(".");
}
builder.append(" ");
}
if(authors != null && authors.length() > 0) {
authors = "<B>" + authors + "</B>; ";
} else {
authors = "";
String authors = getAuthorString();
if(!Utils.isEmpty(authors)) {
builder.append("<B>")
.append(authors)
.append("</B>. ");
}
if(source != null && source.length() > 0) {
String source = getSource();
if(!Utils.isEmpty(source)) {
if(source.startsWith("http://")) {
source = "<A href='" + source + "'>" + source + "</A>; ";
builder.append("<A href='")
.append(source)
.append("'>")
.append(source)
.append("</A>. ");
} else {
source = "<I>" + source + "</I>; ";
builder.append("<I>")
.append(source)
.append("</I>. ");
}
}
if(year != null && year.length() > 0) {
year += "; ";
String year = getYear();
if(!Utils.isEmpty(year)) {
builder.append(year)
.append(". ");
}
if(pmid != null && pmid.length() > 0) {
pmid = "<A href='" + PUBMED_URL + pmid + "'>" +
"PubMed" + "</A>";
} else {
pmid = "";
String pmid = getPubmedId();
if(!Utils.isEmpty(pmid)) {
builder.append("<A href='" + PUBMED_URL)
.append(pmid)
.append("'>PubMed ")
.append(pmid)
.append("</A>.");
}
return title + authors + source + year + pmid;
return builder.toString();
}
}
20 changes: 11 additions & 9 deletions modules/org.pathvisio.gui/src/org/pathvisio/gui/PathwayFileFilter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,15 +43,17 @@ public boolean accept(File f) {
if(f.isDirectory()) return true;

String fn = f.toString();
int i = fn.lastIndexOf('.');
if(i > 0) {
String ext = fn.substring(i + 1);
for(String impExt : exts) {
if(impExt.equalsIgnoreCase(ext)) {
return true;
}
}
}
if (fn != null) {
int i = fn.lastIndexOf('.');
if (i > 0) {
String ext = fn.substring(i + 1);
for (String impExt : exts) {
if (impExt.equalsIgnoreCase(ext)) {
return true;
}
}
}
}
return false;
}

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6 changes: 4 additions & 2 deletions modules/org.pathvisio.gui/src/org/pathvisio/gui/handler/PropertyView.java
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Original file line number Diff line number Diff line change
Expand Up @@ -160,8 +160,10 @@ public void setValue(Object value) {
vPathway.getUndoManager().newAction (
"Change " + type + " property");
}
for(PathwayElement e : elements) {
e.setPropertyEx(type, value);
PathwayElement[] pathwayElements = new PathwayElement[elements.size()];
elements.toArray(pathwayElements);
for (PathwayElement pe : pathwayElements) {
pe.setPropertyEx(type, value);
}
}
}
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126 changes: 63 additions & 63 deletions tools/KeggConverter/examples/map00031.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -102,61 +102,61 @@
<entry id="22" name="ec:2.2.1.2" type="enzyme" map="3"
link="http://www.genome.jp/dbget-bin/show_pathway?map00030+2.2.1.2"/>
<entry id="23" name="ec:4.1.2.9" type="enzyme" map="3"
link="http://www.genome.jp/dbget-bin/show_pathway?map00030+4.1.2.9"/>
<entry id="24" name="ec:1.2.1.5" type="enzyme" reaction="rn:R04891 rn:R04892"
link="http://www.genome.jp/dbget-bin/www_bget?enzyme+1.2.1.5">
<graphics name="1.2.1.5" fgcolor="#000000" bgcolor="#FFFFFF"
type="rectangle" x="1390" y="531" width="45" height="17"/>
</entry>
<entry id="25" name="ec:2.1.1.6" type="enzyme" reaction="rn:R02534"
link="http://www.genome.jp/dbget-bin/www_bget?enzyme+2.1.1.6">
<graphics name="2.1.1.6" fgcolor="#000000" bgcolor="#FFFFFF"
type="rectangle" x="1206" y="409" width="45" height="17"/>
</entry>
<entry id="187" name="cpd:C05589" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C05589">
<graphics name="C05589" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1271" y="409" width="8" height="8"/>
</entry>
<entry id="190" name="cpd:C05583" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C05583">
<graphics name="C05583" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1390" y="447" width="8" height="8"/>
</entry>
<entry id="30" name="ec:1.4.3.4" type="enzyme" reaction="rn:R04893"
link="http://www.genome.jp/dbget-bin/www_bget?enzyme+1.4.3.4">
<graphics name="1.4.3.4" fgcolor="#000000" bgcolor="#FFFFFF"
type="rectangle" x="1329" y="409" width="45" height="17"/>
</entry>
<entry id="33" name="ec:1.2.1.5" type="enzyme" reaction="rn:R04891 rn:R04892"
link="http://www.genome.jp/dbget-bin/www_bget?enzyme+1.2.1.5">
<graphics name="1.2.1.5" fgcolor="#000000" bgcolor="#FFFFFF"
type="rectangle" x="1390" y="531" width="45" height="17"/>
</entry>
<entry id="186" name="cpd:C00547" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C00547">
<graphics name="C00547" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1156" y="447" width="8" height="8"/>
</entry>
<entry id="32" name="ec:1.14.18.-" type="enzyme" reaction="rn:R06612"
link="http://www.genome.jp/dbget-bin/www_bget?enzyme+1.14.18.-">
<graphics name="1.14.18.-" fgcolor="#000000" bgcolor="#FFFFFF"
type="rectangle" x="1352" y="311" width="45" height="17"/>
</entry>
<entry id="191" name="cpd:C05584" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C05584">
<graphics name="C05584" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1390" y="607" width="8" height="8"/>
</entry>
<entry id="172" name="cpd:C05606" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C05606">
<graphics name="C05606" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1412" y="258" width="8" height="8"/>
</entry>
<entry id="51" name="cpd:C04185" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C04185">
<graphics name="C04185" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1289" y="312" width="8" height="8"/>
link="http://www.genome.jp/dbget-bin/show_pathway?map00030+4.1.2.9"/>
<entry id="24" name="ec:1.2.1.5" type="enzyme" reaction="rn:R04891 rn:R04892"
link="http://www.genome.jp/dbget-bin/www_bget?enzyme+1.2.1.5">
<graphics name="1.2.1.5" fgcolor="#000000" bgcolor="#FFFFFF"
type="rectangle" x="1390" y="531" width="45" height="17"/>
</entry>
<entry id="25" name="ec:2.1.1.6" type="enzyme" reaction="rn:R02534"
link="http://www.genome.jp/dbget-bin/www_bget?enzyme+2.1.1.6">
<graphics name="2.1.1.6" fgcolor="#000000" bgcolor="#FFFFFF"
type="rectangle" x="1206" y="409" width="45" height="17"/>
</entry>
<entry id="187" name="cpd:C05589" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C05589">
<graphics name="C05589" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1271" y="409" width="8" height="8"/>
</entry>
<entry id="190" name="cpd:C05583" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C05583">
<graphics name="C05583" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1390" y="447" width="8" height="8"/>
</entry>
<entry id="30" name="ec:1.4.3.4" type="enzyme" reaction="rn:R04893"
link="http://www.genome.jp/dbget-bin/www_bget?enzyme+1.4.3.4">
<graphics name="1.4.3.4" fgcolor="#000000" bgcolor="#FFFFFF"
type="rectangle" x="1329" y="409" width="45" height="17"/>
</entry>
<entry id="33" name="ec:1.2.1.5" type="enzyme" reaction="rn:R04891 rn:R04892"
link="http://www.genome.jp/dbget-bin/www_bget?enzyme+1.2.1.5">
<graphics name="1.2.1.5" fgcolor="#000000" bgcolor="#FFFFFF"
type="rectangle" x="1390" y="531" width="45" height="17"/>
</entry>
<entry id="186" name="cpd:C00547" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C00547">
<graphics name="C00547" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1156" y="447" width="8" height="8"/>
</entry>
<entry id="32" name="ec:1.14.18.-" type="enzyme" reaction="rn:R06612"
link="http://www.genome.jp/dbget-bin/www_bget?enzyme+1.14.18.-">
<graphics name="1.14.18.-" fgcolor="#000000" bgcolor="#FFFFFF"
type="rectangle" x="1352" y="311" width="45" height="17"/>
</entry>
<entry id="191" name="cpd:C05584" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C05584">
<graphics name="C05584" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1390" y="607" width="8" height="8"/>
</entry>
<entry id="172" name="cpd:C05606" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C05606">
<graphics name="C05606" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1412" y="258" width="8" height="8"/>
</entry>
<entry id="51" name="cpd:C04185" type="compound"
link="http://www.genome.jp/dbget-bin/www_bget?compound+C04185">
<graphics name="C04185" fgcolor="#000000" bgcolor="#FFFFFF"
type="circle" x="1289" y="312" width="8" height="8"/>
</entry>
<relation entry1="19" entry2="20" type="ECrel">
<subtype name="compound" value="13"/>
Expand Down Expand Up @@ -220,13 +220,13 @@
<reaction name="rn:R01183" type="reversible">
<substrate name="cpd:C00137"/>
<product name="cpd:C00691"/>
</reaction>
<reaction name="rn:R04893" type="irreversible">
<substrate name="cpd:C05589"/>
<product name="cpd:C05583"/>
</reaction>
<reaction name="rn:R02534" type="irreversible">
<substrate name="cpd:C00547"/>
<product name="cpd:C05589"/>
</reaction>
<reaction name="rn:R04893" type="irreversible">
<substrate name="cpd:C05589"/>
<product name="cpd:C05583"/>
</reaction>
<reaction name="rn:R02534" type="irreversible">
<substrate name="cpd:C00547"/>
<product name="cpd:C05589"/>
</reaction>
</pathway>
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