Ignore:
Timestamp:
Feb 22, 2012, 9:32:28 AM (10 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #360: Changes related to new GUI in BASE 3.1

Location:
extensions/net.sf.basedb.mev/trunk/resources
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.mev/trunk/resources/launch_mev.jsp

    r1416 r1541  
    1 <%-- $Id: launch_mev.jsp 1083 2009-05-18 12:19:18Z nicklas $
     1<%-- $Id$
    22  ------------------------------------------------------------------
    33  Copyright (C) 2009 Nicklas Nordborg
     
    145145    url += '&parameter:saveAs='+encodeURIComponent('<%=HTML.javaScriptEncode(defaultPath+defaultTdmsFileName)%>');
    146146    url += '&parameter:attachToBioAssaySet=true';
    147     Main.openPopup(url, 'CreateTDMSFile', 740, 540);
     147    Main.openPopup(url, 'CreateTDMSFile', 750, 500);
    148148    window.close();
    149149  }
     
    158158    url += '&parameter:saveAs='+encodeURIComponent('<%=HTML.javaScriptEncode(defaultPath+defaultCghFileName)%>');
    159159    url += '&parameter:attachToBioAssaySet=true';
    160     Main.openPopup(url, 'CreateCGHFile', 740, 540);
     160    Main.openPopup(url, 'CreateCGHFile', 750, 500);
    161161    window.close();
    162162  }
     
    164164</base:head>
    165165<base:body>
     166  <h1><%=title%></h1>
    166167
    167168  <form name="mev">
    168   <h3><%=title%></h3>
    169   <div class="boxedbottom">
    170   <table class="form">
    171   <tr>
    172     <td class="prompt" colspan="2">MeV analysis file</td>
    173   </tr>
    174   <tr>
    175     <td><base:button title="Start MeV"
    176       onclick="launchMev('mev.anl')"
    177       image="<%=anlFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>"
    178       disabled="<%=anlFile == null%>"/></td>
    179     <td>
    180     <%
    181     if (anlFile == null)
    182     {
     169  <div class="content bottomborder">
     170
     171  <table class="fullform">
     172    <tbody class="sectionheader">
     173      <tr>
     174        <th colspan="2">MeV analysis file</th>
     175      </tr>
     176    </tbody>
     177    <tbody>
     178      <tr>
     179        <td style="padding-bottom: 1em;"><base:button title="Start MeV"
     180          onclick="launchMev('mev.anl')"
     181          image="<%=anlFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>"
     182          disabled="<%=anlFile == null%>"/></td>
     183        <td style="padding-bottom: 1em;">
     184        <%
     185        if (anlFile == null)
     186        {
     187          %>
     188          There is currently no MeV analysis file associated with the bioassay set.
     189          <%
     190        }
     191        else
     192        {
     193          %>
     194          Start MeV with the current analysis file:<br>
     195          <%=HTML.encodeTags(anlFile.getName())%> <%=Base.getFileLinks(ID, anlFile, root) %>
     196          <%
     197        }
     198        %>
     199        </td>
     200      </tr>
     201    </tbody>
     202    <tbody class="sectionheader">
     203      <tr>
     204        <th colspan="2">TDMS - Tab-delimited multiple sample</th>
     205      </tr>
     206    </tbody>
     207    <tbody>
     208      <tr>
     209        <td><base:button title="Start MeV"
     210          onclick="launchMev('mev.tdms')"
     211          image="<%=tdmsFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>"
     212          disabled="<%=tdmsFile == null%>"/></td>
     213        <td>
     214        <%
     215        if (tdmsFile == null)
     216        {
     217          %>
     218          There is currently no TDMS file associated with the bioassay set.
     219          <%
     220        }
     221        else
     222        {
     223          %>
     224          Start MeV with the current TDMS file:<br>
     225          <%=HTML.encodeTags(tdmsFile.getName())%> <%=Base.getFileLinks(ID, tdmsFile, root) %>
     226          <%
     227        }
     228        %>
     229        </td>
     230      </tr>
     231      <tr>
     232        <td style="padding-bottom: 1em;"><base:button title="Export"
     233          onclick="exportTdms()"
     234          disabled="<%=!allowCreateFile%>"
     235          image="<%=allowCreateFile ? "export.gif" : homeUrl + "/images/export_disabled.gif"%>" /></td>
     236        <td style="padding-bottom: 1em;">
     237        <%
     238        if (allowCreateFile)
     239        {
     240          %>
     241          Export the spot data to a MeV TDMS file that can be opened with MeV.
     242          <%
     243        }
     244        else
     245        {
     246          %>
     247          You don't have enough permissions to create a MeV TDSM file.
     248          <%
     249        }
     250        %>
     251        </td>
     252      </tr>
     253    </tbody>
     254    <tbody class="sectionheader">
     255      <tr>
     256        <th colspan="2">CGH - Comparative genomics hybridization</th>
     257      </tr>
     258    </tbody>
     259    <tbody>
     260      <tr>
     261        <td><base:button title="Start MeV"
     262          onclick="launchMev('mev.cgh')"
     263          image="<%=cghFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>"
     264          disabled="<%=cghFile == null%>"/></td>
     265        <td>
     266        <%
     267        if (cghFile == null)
     268        {
     269          %>
     270          There is currently no CGH file associated with the bioassay set.
     271          <%
     272        }
     273        else
     274        {
     275          %>
     276          Start MeV with the current CGH file:<br>
     277          <%=HTML.encodeTags(cghFile.getName())%> <%=Base.getFileLinks(ID, cghFile, root) %>
     278          <%
     279        }
     280        %>
     281        </td>
     282      </tr>
     283      <tr>
     284        <td><base:button title="Export"
     285          onclick="exportCgh()"
     286          disabled="<%=!canCreateCGHFile%>"
     287          image="<%=canCreateCGHFile ? "export.gif" : homeUrl + "/images/export_disabled.gif"%>" /></td>
     288        <td>
     289        <%
     290        if (canCreateCGHFile)
     291        {
     292          %>
     293          Export the spot data to a MeV CGH file that can be opened with MeV.
     294          <%
     295        }
     296        else
     297        {
     298          %>
     299          You don't have enough permissions to create a MeV CGH file.
     300          <%
     301        }
     302        %>
     303        </td>
     304      </tr>
     305      <%
     306      if (canCreateCGHFile)
     307      {
     308        %>
     309        <tr>
     310          <td style="text-align: right;">-configuration</td>
     311          <td>
     312            <select name="cgh_configuration">
     313            <%
     314            for (PluginConfiguration cfg : cghConfigurations)
     315            {
     316              %>
     317              <option value="<%=cfg.getId()%>"><%=HTML.encodeTags(cfg.getName())%>
     318              <%
     319            }
     320            %>
     321            </select>
     322          </td>
     323        </tr>
     324        <%
     325      }
    183326      %>
    184       There is currently no MeV analysis file associated with the bioassay set.
    185       <%
    186     }
    187     else
    188     {
    189       %>
    190       Start MeV with the current analysis file:<br>
    191       <%=HTML.encodeTags(anlFile.getName())%> <%=Base.getFileLinks(ID, anlFile, root) %>
    192       <%
    193     }
    194     %>
    195     </td>
    196   </tr>
    197   <tr>
    198     <td class="prompt" colspan="2">TDMS - Tab-delimited multiple sample</td>
    199   </tr>
    200   <tr>
    201     <td><base:button title="Start MeV"
    202       onclick="launchMev('mev.tdms')"
    203       image="<%=tdmsFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>"
    204       disabled="<%=tdmsFile == null%>"/></td>
    205     <td>
    206     <%
    207     if (tdmsFile == null)
    208     {
    209       %>
    210       There is currently no TDMS file associated with the bioassay set.
    211       <%
    212     }
    213     else
    214     {
    215       %>
    216       Start MeV with the current TDMS file:<br>
    217       <%=HTML.encodeTags(tdmsFile.getName())%> <%=Base.getFileLinks(ID, tdmsFile, root) %>
    218       <%
    219     }
    220     %>
    221     </td>
    222   </tr>
    223   <tr>
    224     <td><base:button title="Export"
    225       onclick="exportTdms()"
    226       disabled="<%=!allowCreateFile%>"
    227       image="<%=allowCreateFile ? "export.gif" : homeUrl + "/images/export_disabled.gif"%>" /></td>
    228     <td>
    229     <%
    230     if (allowCreateFile)
    231     {
    232       %>
    233       Export the spot data to a MeV TDMS file that can be opened with MeV.
    234       <%
    235     }
    236     else
    237     {
    238       %>
    239       You don't have enough permissions to create a MeV TDSM file.
    240       <%
    241     }
    242     %>
    243     </td>
    244   </tr>
    245   <tr>
    246     <td class="prompt" colspan="2">CGH - Comparative genomics hybridization</td>
    247   </tr>
    248   <tr>
    249     <td><base:button title="Start MeV"
    250       onclick="launchMev('mev.cgh')"
    251       image="<%=cghFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>"
    252       disabled="<%=cghFile == null%>"/></td>
    253     <td>
    254     <%
    255     if (cghFile == null)
    256     {
    257       %>
    258       There is currently no CGH file associated with the bioassay set.
    259       <%
    260     }
    261     else
    262     {
    263       %>
    264       Start MeV with the current CGH file:<br>
    265       <%=HTML.encodeTags(cghFile.getName())%> <%=Base.getFileLinks(ID, cghFile, root) %>
    266       <%
    267     }
    268     %>
    269     </td>
    270   </tr>
    271   <tr>
    272     <td><base:button title="Export"
    273       onclick="exportCgh()"
    274       disabled="<%=!canCreateCGHFile%>"
    275       image="<%=canCreateCGHFile ? "export.gif" : homeUrl + "/images/export_disabled.gif"%>" /></td>
    276     <td>
    277     <%
    278     if (canCreateCGHFile)
    279     {
    280       %>
    281       Export the spot data to a MeV CGH file that can be opened with MeV.
    282       <%
    283     }
    284     else
    285     {
    286       %>
    287       You don't have enough permissions to create a MeV CGH file.
    288       <%
    289     }
    290     %>
    291     </td>
    292   </tr>
    293   <%
    294   if (canCreateCGHFile)
    295   {
    296     %>
    297     <tr>
    298       <td style="text-align: right;">-configuration</td>
    299       <td>
    300         <select name="cgh_configuration">
    301         <%
    302         for (PluginConfiguration cfg : cghConfigurations)
    303         {
    304           %>
    305           <option value="<%=cfg.getId()%>"><%=HTML.encodeTags(cfg.getName())%>
    306           <%
    307         }
    308         %>
    309         </select>
    310       </td>
     327    </tbody>
     328    <tr class="dynamic">
     329      <td></td>
     330      <td></td>
    311331    </tr>
    312     <%
    313   }
    314   %>
    315332  </table>
    316333  </div>
    317334  </form>
    318335
    319   <table align="center">
    320   <tr>
    321     <td><base:button onclick="window.close();" title="Close" /></td>
    322   </tr>
    323   </table>
     336  <base:buttongroup subclass="dialogbuttons">
     337    <base:button onclick="window.close();" title="Close" />
     338  </base:buttongroup>
    324339
    325340</base:body>
  • extensions/net.sf.basedb.mev/trunk/resources/options.jsp

    r1416 r1541  
    4141%>
    4242<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
    43 <%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
    4443
    4544<%
     
    6968<base:body>
    7069
     70  <h1>MeV Launcher options for <%=HTML.encodeTags(user.getName())%></h1>
    7171  <form action="submit.jsp?ID=<%=ID%>" method="post" name="mevoptions" onsubmit="return false;">
    7272  <input type=hidden name="cmd" value="SaveOptions">
    7373 
    74   <h3 class="docked">MeV Launcher options for <%=HTML.encodeTags(user.getName())%></h3>
    75   <t:tabcontrol id="mevoptions"
    76     contentstyle="<%="height: "+(int)(scale*240)+"px;"%>"
    77     position="bottom">
    78  
    79   <t:tab id="option" title="MeV options" validate="validateOptions()">
    80 
    81     <table class="form" cellspacing=0>
    82     <tr>
    83       <td colspan="2">
    84         <i>Specify the amount of memory the Java Virtual Machine
    85         for MeV is allowed to use. The default value is 512MB. We don't
    86         recommend a lower value, but you may increase the value if your
    87         computer has memory to spare.</i>
    88       </td>
    89     </tr>
    90     <tr>
    91       <td class="prompt">JVM max memory</td>
     74  <div class="content filled">
     75    <div>
     76    <table class="fullform bottomborder">
     77    <tr style="height: 3em;">
     78      <th>JVM max memory</td>
    9279      <td><input class="text" type="text" name="maxMemory"
    93           value="<%=maxMemory%>" size="8" maxlength="6"
     80          value="<%=maxMemory%>" style="width: 12em;" maxlength="6"
    9481          onkeypress="return Numbers.integerOnly(event)"> MB</td>
    9582    </tr>
    9683    </table>
     84    </div>
     85   
     86    <div class="messagecontainer note">
     87      Specify the amount of memory the Java Virtual Machine for MeV is allowed to use.
     88      The default value is 512MB. We don't recommend a lower value, but you may increase the value
     89      if your computer has memory to spare.
     90    </div>
    9791
    98   </t:tab>
    99   </t:tabcontrol>
    100   <p>
    101   <table align="center">
    102   <tr>
    103     <td width="50%"><base:button onclick="saveSettings();" title="Save" /></td>
    104     <td width="50%"><base:button onclick="window.close();" title="Cancel" /></td>
    105   </tr>
    106   </table>
     92  </div>
     93
     94  <base:buttongroup subclass="dialogbuttons">
     95    <base:button onclick="saveSettings();" title="Save" />
     96    <base:button onclick="window.close();" title="Cancel" />
     97  </base:buttongroup>
     98 
    10799</base:body>
    108100</base:page>
  • extensions/net.sf.basedb.mev/trunk/resources/scripts/mev.jsp

    r1083 r1541  
    1515    url += '?ID='+getSessionId();
    1616    url += '&bioassayset_id=' + bioAssaySetId;
    17     Main.openPopup(url, 'LaunchMev', 500, 340);
     17    Main.openPopup(url, 'LaunchMev', 600, 400);
    1818  }
    1919
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