https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=Coder Coder - Revision history 2026-04-30T04:16:59Z Revision history for this page on the wiki MediaWiki 1.20.3 https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Coder&diff=6454&oldid=prev Kdahlquist: /* Milestone 1 */ removed extra GenMAPP URL reference 2013-11-26T19:13:10Z <p>‎<span dir="auto"><span class="autocomment">Milestone 1: </span> removed extra GenMAPP URL reference</span></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 19:13, 26 November 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 20:</td> <td colspan="2" class="diff-lineno">Line 20:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#*** Note that you need to use 32-bit Java</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#*** Note that you need to use 32-bit Java</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#* GenMAPP (http://genmapp.org)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#* GenMAPP (http://genmapp.org)</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>#** We will be using GenMAPP and MAPPFinder version 2.1 <del class="diffchange diffchange-inline">(http://genmapp.org)</del>.&#160; This software is already installed on the Windows machines in the Keck lab annex and in the Seaver 120 computer lab.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>#** We will be using GenMAPP and MAPPFinder version 2.1.&#160; This software is already installed on the Windows machines in the Keck lab annex and in the Seaver 120 computer lab.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#*** This version is now called &quot;GenMAPP Classic&quot; and can be downloaded [http://www.genmapp.org/download_v2.1.php from this page].</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#*** This version is now called &quot;GenMAPP Classic&quot; and can be downloaded [http://www.genmapp.org/download_v2.1.php from this page].</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#*** Follow the instructions in the installer.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#*** Follow the instructions in the installer.</div></td></tr> </table> Kdahlquist https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Coder&diff=6453&oldid=prev Kdahlquist: /* Milestone 1 */ put in more specific instructions for downloading genmapp 2013-11-26T19:12:43Z <p>‎<span dir="auto"><span class="autocomment">Milestone 1: </span> put in more specific instructions for downloading genmapp</span></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 19:12, 26 November 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 20:</td> <td colspan="2" class="diff-lineno">Line 20:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#*** Note that you need to use 32-bit Java</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#*** Note that you need to use 32-bit Java</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#* GenMAPP (http://genmapp.org)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#* GenMAPP (http://genmapp.org)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#** We will be using GenMAPP and MAPPFinder version 2.1 (http://genmapp.org).&#160; This software is already installed on the Windows machines in the Keck lab annex and in the Seaver 120 computer lab.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#*** This version is now called &quot;GenMAPP Classic&quot; and can be downloaded [http://www.genmapp.org/download_v2.1.php from this page].</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#*** Follow the instructions in the installer.</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#*** During installation, the installer will open a window called the GenMAPP Data Acquisition Tool.&#160; It will not function because it cannot connect to the server.&#160; This is OK.</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#* XMLPipeDB &#039;&#039;match&#039;&#039; utility for counting IDs in XML files</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#* XMLPipeDB &#039;&#039;match&#039;&#039; utility for counting IDs in XML files</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#* Microsoft Access or any other tool that can read .mdb files</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>#* Microsoft Access or any other tool that can read .mdb files</div></td></tr> </table> Kdahlquist https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Coder&diff=5536&oldid=prev Dondi: /* Java Project Setup */ Add instructions on JDK. 2013-11-14T17:18:28Z <p>‎<span dir="auto"><span class="autocomment">Java Project Setup: </span> Add instructions on JDK.</span></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 17:18, 14 November 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 89:</td> <td colspan="2" class="diff-lineno">Line 89:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Java Project Setup ===</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Java Project Setup ===</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"># Make sure that Eclipse is using a &#039;&#039;&#039;&#039;&#039;JDK&#039;&#039;&#039;&#039;&#039; (Java Development Kit) and not a &#039;&#039;JRE&#039;&#039; (Java Runtime Environment).&#160; To verify this, go to &#039;&#039;Window&#039;&#039; &gt; &#039;&#039;Preferences&#039;&#039;, click on &#039;&#039;Java&#039;&#039;, click on &#039;&#039;Installed JREs&#039;&#039;, and make sure that the checked environment has &#039;&#039;&#039;JDK&#039;&#039;&#039; in it.&#160; If not, you may need to add the environment (on Windows, it lives in &lt;code&gt;C:\Program Files\Java&lt;/code&gt;) then check on it.</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Upon a successful checkout, you should have a &#039;&#039;gmbuilder&#039;&#039; Java project in Eclipse.&#160; Make sure that you are in the &#039;&#039;Java&#039;&#039; perspective by choosing &#039;&#039;Window&#039;&#039; &gt; &#039;&#039;Open Perspective&#039;&#039; &gt; &#039;&#039;Java&#039;&#039; (or choosing &#039;&#039;Java&#039;&#039; from &#039;&#039;Other...&#039;&#039; if &#039;&#039;Java&#039;&#039; is not already in the &#039;&#039;Open Perspective&#039;&#039; submenu).</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Upon a successful checkout, you should have a &#039;&#039;gmbuilder&#039;&#039; Java project in Eclipse.&#160; Make sure that you are in the &#039;&#039;Java&#039;&#039; perspective by choosing &#039;&#039;Window&#039;&#039; &gt; &#039;&#039;Open Perspective&#039;&#039; &gt; &#039;&#039;Java&#039;&#039; (or choosing &#039;&#039;Java&#039;&#039; from &#039;&#039;Other...&#039;&#039; if &#039;&#039;Java&#039;&#039; is not already in the &#039;&#039;Open Perspective&#039;&#039; submenu).</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Double-click on the &#039;&#039;gmbuilder&#039;&#039; folder (or whatever you called it) to view its contents.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Double-click on the &#039;&#039;gmbuilder&#039;&#039; folder (or whatever you called it) to view its contents.</div></td></tr> </table> Dondi https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Coder&diff=5016&oldid=prev Kdahlquist: commented out redlink to beta 60 release.zip 2013-11-06T18:44:49Z <p>commented out redlink to beta 60 release.zip</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 18:44, 6 November 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 257:</td> <td colspan="2" class="diff-lineno">Line 257:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Mark the current release as the default Windows download by selecting the small i button next to .zip.</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div># Mark the current release as the default Windows download by selecting the small i button next to .zip.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">&lt;!--</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==GenMAPP Beta Release Zip==</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>==GenMAPP Beta Release Zip==</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Media:Gmbuilder-2.0b60.zip‎|Gmbuilder-2.0b60.zip‎]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Media:Gmbuilder-2.0b60.zip‎|Gmbuilder-2.0b60.zip‎]]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">--&gt;</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Group Projects]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Group Projects]]</div></td></tr> </table> Kdahlquist  
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''.  If you don't see this, double-check your installation of Subclipse.
 
# Go to Eclipse’s menu bar’s ''Window'' > ''Open Perspective'' and choose ''SVN Repository Exploring'' either from the ''Open Perspective'' submenu if it is there, or from ''Other...''.  If you don't see this, double-check your installation of Subclipse.
 
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
 
# Define a new Subversion repository by clicking on the ''Add Repository'' button (this is the icon with the little yellow canister with small ''SVN'' and ''+'' badges to its right).
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Stack trace:
#0 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(480): _DiffEngine->_diag()
#1 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(291): _DiffEngine->_compareseq()
#2 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(175): _DiffEngine->diff_local()
#3 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(653): _DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(820): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(1240): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(1458): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(952): TableDiffFormatter->_changed()
#8 /apps/xmlpipedb/biodb/fall2013/includes/diff/DairikiDiff.php(895): DiffFormatter->_block()
#9 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(765): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(655): DifferenceEngine->generateDiffBody()
#11 /apps/xmlpipedb/biodb/fall2013/includes/diff/DifferenceEngine.php(593): DifferenceEngine->getDiffBody()
#12 /apps/xmlpipedb/biodb/fall2013/includes/FeedUtils.php(147): DifferenceEngine->getDiff()
#13 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(303): FeedUtils::formatDiffRow()
#14 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(268): HistoryAction->feedItem()
#15 /apps/xmlpipedb/biodb/fall2013/includes/actions/HistoryAction.php(121): HistoryAction->feed()
#16 /apps/xmlpipedb/biodb/fall2013/includes/Action.php(541): HistoryAction->onView()
#17 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(427): FormlessAction->show()
#18 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(304): MediaWiki->performAction()
#19 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(536): MediaWiki->performRequest()
#20 /apps/xmlpipedb/biodb/fall2013/includes/Wiki.php(446): MediaWiki->main()
#21 /apps/xmlpipedb/biodb/fall2013/index.php(59): MediaWiki->run()
#22 {main}